diff --git a/clinvar_data/conversion/dict_to_pb.py b/clinvar_data/conversion/dict_to_pb.py index 60eed4c..4688b47 100644 --- a/clinvar_data/conversion/dict_to_pb.py +++ b/clinvar_data/conversion/dict_to_pb.py @@ -1375,6 +1375,9 @@ def convert_trait_relationship(cls, value: dict[str, Any]) -> Trait.TraitRelatio tag_trait_relationship["Name"], dict ), "never seen more than once in XML" names = [ConvertGenericSetElement.xmldict_data_to_pb(tag_trait_relationship, "Name")] + sources: list[str] = [] + if "Source" in tag_trait_relationship: + sources = cls.ensure_list(tag_trait_relationship["Source"]) # Parse out Citation, XRef, Comment tags. cxcs = cls.parse_citations_xrefs_comments(tag_trait_relationship) @@ -1384,6 +1387,7 @@ def convert_trait_relationship(cls, value: dict[str, Any]) -> Trait.TraitRelatio citations=cxcs.citations, xrefs=cxcs.xrefs, comments=cxcs.comments, + sources=sources, ) @classmethod @@ -1928,14 +1932,11 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AggregateClassificationSet germline_classification = ConvertAggregatedGermlineClassification.xmldict_data_to_pb( {"GermlineClassification": tag_classifications["GermlineClassification"]} ) - somatic_clinical_impacts: list[AggregatedSomaticClinicalImpact] | None = None + somatic_clinical_impact: AggregatedSomaticClinicalImpact | None = None if "SomaticClinicalImpact" in tag_classifications: - somatic_clinical_impacts = [ - ConvertAggregatedSomaticClinicalImpact.xmldict_data_to_pb( - {"SomaticClinicalImpact": element} - ) - for element in cls.ensure_list(tag_classifications["SomaticClinicalImpact"]) - ] + somatic_clinical_impact = ConvertAggregatedSomaticClinicalImpact.xmldict_data_to_pb( + {"SomaticClinicalImpact": tag_classifications["SomaticClinicalImpact"]} + ) oncogenicity_classification: AggregatedOncogenicityClassification | None = None if "OncogenicityClassification" in tag_classifications: oncogenicity_classification = ( @@ -1950,7 +1951,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AggregateClassificationSet return AggregateClassificationSet( germline_classification=germline_classification, - somatic_clinical_impacts=somatic_clinical_impacts, + somatic_clinical_impact=somatic_clinical_impact, oncogenicity_classification=oncogenicity_classification, ) @@ -2187,9 +2188,9 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> ClassificationScv: ) ) germline_classification: str | None = tag_classification.get("GermlineClassification") - somatic_clinical_impacts: ClassificationScv.SomaticClinicalImpact | None = None + somatic_clinical_impact: ClassificationScv.SomaticClinicalImpact | None = None if "SomaticClinicalImpact" in tag_classification: - somatic_clinical_impacts = cls.convert_somatic_clinical_impact( + somatic_clinical_impact = cls.convert_somatic_clinical_impact( {"SomaticClinicalImpact": tag_classification["SomaticClinicalImpact"]} ) oncogenicity_classification: str | None = tag_classification.get( @@ -2217,7 +2218,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> ClassificationScv: return ClassificationScv( review_status=review_status, germline_classification=germline_classification, - somatic_clinical_impacts=somatic_clinical_impacts, + somatic_clinical_impact=somatic_clinical_impact, oncogenicity_classification=oncogenicity_classification, explanation_of_classification=explanation_of_classification, classification_scores=classification_scores, @@ -3457,12 +3458,10 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AlleleScv: # noqa: C901 cls.convert_gene({"Gene": entry}) for entry in cls.ensure_list(tag_sa["GeneList"]["Gene"]) ] - names: list[OtherName] | None = None + name: OtherName | None = None if "Name" in tag_sa: - names = [ - ConvertOtherName.xmldict_data_to_pb({"Name": entry}) - for entry in cls.ensure_list(tag_sa["Name"]) - ] + assert isinstance(tag_sa["Name"], (dict, str)), f"is: {tag_sa['Name']}" + name = ConvertOtherName.xmldict_data_to_pb({"Name": tag_sa["Name"]}) variant_type: str | None = tag_sa.get("VariantType") location: Location | None = None if "Location" in tag_sa: @@ -3545,7 +3544,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AlleleScv: # noqa: C901 return AlleleScv( genes=genes, - names=names, + name=name, variant_type=variant_type, location=location, other_names=other_names, @@ -3589,9 +3588,9 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> HaplotypeScv: ConvertOtherName.xmldict_data_to_pb({"Name": entry}) for entry in cls.ensure_list(tag_genotype["OtherNameList"]["Name"]) ] - classification: AggregateClassificationSet | None = None + classifications: AggregateClassificationSet | None = None if "Classification" in tag_genotype: - classification = ConvertAggregateClassificationSet.xmldict_data_to_pb( + classifications = ConvertAggregateClassificationSet.xmldict_data_to_pb( tag_genotype["Classification"] ) functional_consequences: list[FunctionalConsequence] | None = None @@ -3638,7 +3637,7 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> HaplotypeScv: simple_alleles=simple_alleles, name=name, other_names=other_names, - classification=classification, + classifications=classifications, functional_consequences=functional_consequences, attributes=attributes, citations=citations, @@ -4105,12 +4104,12 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> ClinicalAssertion: # noqa: ConvertClinicalAssertionRecordHistory.xmldict_data_to_pb({"Replaced": entry}) for entry in cls.ensure_list(tag_ca["ReplacedList"]["Replaced"]) ] - classifications: list[ClassificationScv] | None = None + classifications: ClassificationScv | None = None if "Classification" in tag_ca: - classifications = [ - ConvertClassificationScv.xmldict_data_to_pb({"Classification": entry}) - for entry in cls.ensure_list(tag_ca["Classification"]) - ] + assert isinstance(tag_ca["Classification"], dict) + classifications = ConvertClassificationScv.xmldict_data_to_pb( + {"Classification": tag_ca["Classification"]} + ) assertion: Assertion.ValueType = ConvertAssertion.xmldict_data_to_pb(tag_ca["Assertion"]) attributes: list[ClinicalAssertion.AttributeSetElement] | None = None if "AttributeSet" in tag_ca: diff --git a/clinvar_data/extract_vars.py b/clinvar_data/extract_vars.py index 677f070..3724cc4 100644 --- a/clinvar_data/extract_vars.py +++ b/clinvar_data/extract_vars.py @@ -84,9 +84,9 @@ def thin_out_aggregate_classification_set( if result.HasField("germline_classification"): for key in ("xrefs", "citations", "history_records", "conditions"): result.germline_classification.ClearField(key) - for somatic_clinical_impacts in result.somatic_clinical_impacts: + if result.HasField("somatic_clinical_impact"): for key in ("xrefs", "citations", "history_records", "conditions"): - somatic_clinical_impacts.ClearField(key) + result.somatic_clinical_impact.ClearField(key) if result.HasField("oncogenicity_classification"): for key in ("xrefs", "citations", "history_records", "conditions"): result.oncogenicity_classification.ClearField(key) diff --git a/clinvar_data/models.py b/clinvar_data/models.py deleted file mode 100644 index 48d25b1..0000000 --- a/clinvar_data/models.py +++ /dev/null @@ -1,2878 +0,0 @@ -"""Support for representing ClinVar data from XSD file using pydantic""" - -import datetime -import enum -import typing - -from dateutil.parser import parse as parse_datetime -from pydantic import BaseModel, ConfigDict - -T = typing.TypeVar("T") - - -def extract_text(element: typing.Any) -> typing.Optional[str]: - """Extract text from a string or dict with ``#text`` key""" - if element is None: - return element - elif isinstance(element, str): - return element - else: - return element["#text"] - - -def force_list(value: typing.Union[T, typing.List[T]]) -> typing.List[T]: - """Helper value that wraps atomic values in a list""" - if isinstance(value, list): - return value - else: - return [value] - - -@enum.unique -class ClinVarAccessionType(enum.Enum): - """ClinVar accession type""" - - RCV = "RCV" - - -@enum.unique -class RecordStatus(enum.Enum): - """Enumeration with ``ClinVarSet.record_status``""" - - CURRENT = "current" - REPLACED = "replaced" - REMOVED = "removed" - - -@enum.unique -class Status(enum.Enum): - """Corresponds to ``typeStatus``""" - - CURRENT = "current" - COMPLETED_AND_RETIRED = "completed and retired" - DELETE = "delete" - IN_DEVELOPMENT = "in development" - RECLASSIFIED = "reclassified" - REJECT = "reject" - SECONDARY = "secondary" - SUPPRESSED = "suppressed" - UNDER_REVIEW = "under review" - - -class Xref(BaseModel): - """This structure is used to represent how an object described in the submission relates to - objects in other databases. - """ - - model_config = ConfigDict(frozen=True) - - #: The database name - db: str - #: The ID of the xref - id: str - #: Optional type of the xref - type: typing.Optional[str] = None - #: Optional URL of the xref - url: typing.Optional[str] = None - #: Optional status of the xref - status: typing.Optional[Status] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Xref": - return Xref( - db=json_data["@DB"], - id=json_data["@ID"], - type=json_data.get("@Type"), - url=json_data.get("@URL"), - status=Status(json_data["@Status"]) if json_data.get("@Status") else None, - ) - - -@enum.unique -class ReviewStatus(enum.Enum): - """The values of review status are used to build the 'star ratings' displayed on the - ClinVar public site. - - - 0 stars: a conflict or not classified by submitter - - 1 star: classified by single submitter - - 2 stars: classified by multiple submitters - - 3 stars: reviewed by expert panel - - 4 stars: reviewed by professional society - - In the case that a submission was flagged as duplicate, ``FLAGGED_SUBMISSION`` is used. - When no unflagged submission is found, ``NO_UNFLAGGED_CLASSIFICATION`` is used. - """ - - NO_ASSERTION_PROVIDED = "no assertion provided" - NO_ASSERTION_CRITERIA_PROVIDED = "no assertion criteria provided" - CRITERIA_PROVIDED_SINGLE_SUBMITTER = "criteria provided, single submitter" - CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS = "criteria provided, multiple submitters, no conflicts" - CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = "criteria provided, conflicting interpretations" - REVIEWED_BY_EXPERT_PANEL = "reviewed by expert panel" - PRACTICE_GUIDELINE = "practice guideline" - FLAGGED_SUBMISSION = "flagged submission" - NO_UNFLAGGED_CLASSIFICATION = "no classifications from unflagged records" - - -@enum.unique -class ClinicalSignificanceDescription(enum.Enum): - """Allowed values for clinical significance description""" - - AFFECTS = "affects" - BENIGN = "benign" - ESTABLISHED_RISK_ALLELE = "established risk allele" - LIKELY_BENIGN = "likely benign" - LIKELY_PATHOGENIC = "likely pathogenic" - LIKELY_PATHOGENIC_LOW_PENETRANCE = "likely pathogenic, low penetrance" - LIKELY_RISK_ALLELE = "likely risk allele" - PATHOGENIC = "pathogenic" - PATHOGENIC_LOW_PENETRANCE = "pathogenic, low penetrance" - UNCERTAIN_RISK_ALLELE = "uncertain risk allele" - UNCERTAIN_SIGNIFICANCE = "uncertain significance" - ASSOCIATION = "association" - ASSOCIATION_NOT_FOUND = "association not found" - CONFERS_SENSITIVITY = "confers sensitivity" - CONFLICTING_DATA_FROM_SUBMITTERS = "conflicting data from submitters" - DRUG_RESPONSE = "drug response" - NOT_PROVIDED = "not provided" - OTHER = "other" - PROTECTIVE = "protective" - RISK_FACTOR = "risk factor" - - @property - def is_canonical_acmg(self) -> bool: - return self in ( - ClinicalSignificanceDescription.BENIGN, - ClinicalSignificanceDescription.LIKELY_BENIGN, - ClinicalSignificanceDescription.UNCERTAIN_SIGNIFICANCE, - ClinicalSignificanceDescription.LIKELY_PATHOGENIC, - ClinicalSignificanceDescription.PATHOGENIC, - ) - - @property - def acmg_code(self) -> typing.Optional[int]: - return { - ClinicalSignificanceDescription.BENIGN: 1, - ClinicalSignificanceDescription.LIKELY_BENIGN: 2, - ClinicalSignificanceDescription.UNCERTAIN_SIGNIFICANCE: 3, - ClinicalSignificanceDescription.LIKELY_PATHOGENIC: 4, - ClinicalSignificanceDescription.PATHOGENIC: 5, - }.get(self) - - @classmethod - def from_the_wild(cls, str) -> "ClinicalSignificanceDescription": - """Convert values "from the wild" where sometimes invalid values are used. - - These are converted to ``Other``. - """ - try: - return ClinicalSignificanceDescription(str) - except ValueError: - return ClinicalSignificanceDescription.OTHER - - -@enum.unique -class CommentType(enum.Enum): - """Types of comments""" - - PUBLIC = "public" - CONVERTED_BY_NCBI = "ConvertedByNCBI" - MISSING_FROM_ASSEMBLY = "MissingFromAssembly" - GENOMIC_LOCATION_NOT_ESTABLISHED = "GenomicLocationNotEstablished" - LOCATION_ON_GENOME_AND_PRODUCT_NOT_ALIGNED = "LocationOnGenomeAndProductNotAligned" - DELETION_COMMENT = "DeletionComment" - MERGE_COMMENT = "MergeComment" - ASSEMBLY_SPECIFIC_ALLELE_DEFINITON = "AssemblySpecificAlleleDefinition" - ALIGNMENT_GAP_MAKES_APPEAR_INCONSISTENT = "AlignmentGapMakesAppearInconsistent" - EXPLANATION_OF_INTERPRETATION = "ExplanationOfInterpretation" - FLAGGED_COMMENT = "FlaggedComment" - - -class Comment(BaseModel): - """A structure to support reporting unformatted content""" - - model_config = ConfigDict(frozen=True) - - #: The comment's content. - text: str - #: An optional type of the comment. - type: typing.Optional[CommentType] = None - #: An optional datasource name. - datasource: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Comment": - if isinstance(json_data, str): - return Comment(text=json_data) - else: - return Comment( - type=CommentType(json_data["@Type"]) if json_data.get("@Type") else None, - datasource=json_data.get("@DataSource"), - text=json_data["#text"], - ) - - -class CitationIdentifier(BaseModel): - """Type for a citation identifier""" - - model_config = ConfigDict(frozen=True) - - #: The identifier source. - source: str - #: The identifier value. - value: str - - @classmethod - def from_json_data(cls, json_data: dict) -> "CitationIdentifier": - return CitationIdentifier( - source=json_data["@Source"], - value=json_data["#text"], - ) - - -class Citation(BaseModel): - """Type for a citation""" - - model_config = ConfigDict(frozen=True) - - #: Citation identifiers. - ids: typing.List[CitationIdentifier] = [] - #: Citation type. - type: typing.Optional[str] = None - #: Corresponds to the abbreviation reported by GTR - abbrev: typing.Optional[str] = None - #: Optional citation URL - url: typing.Optional[str] = None - #: Optional citation text. - citation_text: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Citation": - return Citation( - ids=[ - CitationIdentifier.from_json_data(raw_identifier) - for raw_identifier in force_list(json_data.get("ID", [])) - ], - type=json_data.get("@Type"), - abbrev=json_data.get("@Abbrev"), - url=json_data.get("URL"), - citation_text=json_data.get("CitationText"), - ) - - -@enum.unique -class AssertionTypeSCV(enum.Enum): - """The assertion types available for SCV records""" - - VARIATION_TO_DISEASE = "variation to disease" - VARIATION_IN_MODIFIER_GENE_TO_DISEASE = "variation in modifier gene to disease" - CONFERS_SENSITIVITY = "confers sensitivity" - CONFERS_RESISTANCE = "confers resistance" - VARIANT_TO_NAMED_PROTEIN_EFFECT = "variant to named protein" - VARIATION_TO_INCLUDED_DISEASE = "variation to included disease" - - -class CustomAssertionScore(BaseModel): - """A custom assertion score""" - - model_config = ConfigDict(frozen=True) - - #: Score value - value: float - #: Scoring scheme - type: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "CustomAssertionScore": - return CustomAssertionScore( - value=float(json_data["#text"]), - type=json_data.get("@type"), - ) - - -class ClinicalSignificanceTypeSCV(BaseModel): - """The clinical significance from the SCV""" - - model_config = ConfigDict(frozen=True) - - #: The review status - review_status: typing.Optional[ReviewStatus] = None - #: We are not providing an enumeration for the values we report for clinical significance within the xsd. - #: The values are maintained here: ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_significance.txt. - descriptions: typing.List[ClinicalSignificanceDescription] = [] - #: Explanation is used only when the description is 'conflicting data from submitters'. - #: The element summarizes the conflict. - explanation: typing.Optional[Comment] = None - #: Explanation for interpretation. - explanation_of_interpretation: typing.Optional[str] = None - #: Custom asertion scores. - custom_assertion_score: typing.List[CustomAssertionScore] = [] - #: Cross-references. - xrefs: typing.List[Xref] = [] - #: Citations - citations: typing.List[Citation] = [] - #: Comments. - comments: typing.List[Comment] = [] - #: Date of last evaluation. - date_last_evaluated: typing.Optional[datetime.date] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinicalSignificanceTypeSCV": - # Handle case of the following:: - # - # \ - # criteria provided, single submitter - # - # In contrast to:: - # - # criteria provided, single submitter - review_status = None - if "ReviewStatus" in json_data: - review_status = ReviewStatus(extract_text(json_data["ReviewStatus"])) - - # Same for the descriptions. - descriptions = [] - for raw_description in force_list(json_data.get("Description", [])): - value = extract_text(raw_description) - if value: - descriptions.append(ClinicalSignificanceDescription.from_the_wild(value.lower())) - - return ClinicalSignificanceTypeSCV( - review_status=review_status, - descriptions=descriptions, - explanation=( - Comment.from_json_data(json_data["Explanation"]) - if json_data.get("Explanation") - else None - ), - explanation_of_interpretation=json_data.get("ExplanationOfInterpretation"), - custom_assertion_score=[ - CustomAssertionScore( - value=float(raw_score["#text"]), - type=raw_score.get("@Type"), - ) - for raw_score in force_list(json_data.get("CustomAssertionScore", [])) - if "#text" in raw_score - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - date_last_evaluated=( - parse_datetime( - json_data["@DateLastEvaluated"], - ).date() - if json_data.get("@DateLastEvaluated") - else None - ), - ) - - -class ClinicalSignificanceRCV(BaseModel): - """The clinical significance from the RCV""" - - model_config = ConfigDict(frozen=True) - - #: The review status - review_status: typing.Optional[ReviewStatus] = None - #: We are not providing an enumeration for the values we report for clinical significance within the xsd. - #: The values are maintained here: ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_significance.txt. - description: typing.Optional[ClinicalSignificanceDescription] = None - #: Explanation is used only when the description is 'conflicting data from submitters'. - #: The element summarizes the conflict. - explanation: typing.Optional[Comment] = None - #: Explanation for interpretation. - explanation_of_interpretation: typing.Optional[str] = None - #: Cross-references. - xrefs: typing.List[Xref] = [] - #: Citations - citations: typing.List[Citation] = [] - #: Comments. - comments: typing.List[Comment] = [] - #: Date of last evaluation. - date_last_evaluated: typing.Optional[datetime.date] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinicalSignificanceRCV": - # Handle case of the following:: - # - # \ - # criteria provided, single submitter - # - # In contrast to:: - # - # criteria provided, single submitter - review_status = None - if "ReviewStatus" in json_data: - review_status = ReviewStatus(extract_text(json_data["ReviewStatus"])) - - # Same for the optional description. - raw_description = extract_text(json_data.get("Description", None)) - description = None - if raw_description: - description = ClinicalSignificanceDescription.from_the_wild(raw_description.lower()) - - return ClinicalSignificanceRCV( - review_status=review_status, - description=description, - explanation=( - Comment.from_json_data(json_data["Explanation"]) - if "Explanation" in json_data - else None - ), - explanation_of_interpretation=json_data.get("ExplanationOfInterpretation"), - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - date_last_evaluated=( - parse_datetime( - json_data["@DateLastEvaluated"], - ).date() - if json_data.get("@DateLastEvaluated") - else None - ), - ) - - -class ReferenceClinVarAccession(BaseModel): - """Accession for a reference ClinVar record""" - - model_config = ConfigDict(frozen=True) - - #: The accession assigned by ClinVar - acc: str - #: A new version of an SCV accession is assigned with an update from the submitter. - #: A new version of an RCV accession is assigned when the set of ClinVarAssertions is - #: changed, either by a change in version or by addition of a new submission. - version: int - #: The accession type - type: ClinVarAccessionType - #: Date of previous update - date_updated: datetime.date - #: Date of record creation. - date_created: datetime.date - - @classmethod - def from_json_data(cls, json_data: dict) -> "ReferenceClinVarAccession": - return ReferenceClinVarAccession( - acc=json_data["@Acc"], - version=int(json_data["@Version"]), - type=ClinVarAccessionType(json_data["@Type"]), - date_updated=parse_datetime(json_data["@DateUpdated"]).date(), - date_created=parse_datetime(json_data["@DateCreated"]).date(), - ) - - -@enum.unique -class ReferenceClinVarAssertionAttributeType(enum.Enum): - """Type for an attribute in a ``ReferenceClinVarAssertion``""" - - MODE_OF_INHERITANCE = "ModeOfInheritance" - PENETRANCE = "Penetrance" - AGE_OF_ONSET = "AgeOfOnset" - - -class ReferenceClinVarAssertionAttribute(BaseModel): - """Attribute for ``ReferenceClnVarAssertion`` - - Corresponds to the ```` elements. - """ - - model_config = ConfigDict(frozen=True) - - #: The attribute's value - value: str - #: The attribute's type - type: ReferenceClinVarAssertionAttributeType - #: The optional integer value provided in ClinVar public XML - integer_value: typing.Optional[int] = None - #: The optional date value provided in ClinVar public XML - date_value: typing.Optional[datetime.date] = None - #: Optional list of citations for this attribute - citations: typing.List[Citation] = [] - #: Optional list of cross-references for this attribute - xrefs: typing.List[Xref] = [] - #: Optional list of comments for this attribute - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ReferenceClinVarAssertionAttribute": - attribute = json_data["Attribute"] - return ReferenceClinVarAssertionAttribute( - # value of tag - value=attribute["#text"], - type=ReferenceClinVarAssertionAttributeType(attribute["@Type"]), - integer_value=int(attribute["@integerValue"]) if "@integerValue" in attribute else None, - date_value=( - parse_datetime(attribute["@dateValue"]) if "@dateValue" in attribute else None - ), - # other data in lists - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class Zygosity(enum.Enum): - """Zygosity options""" - - HOMOZYGOTE = "Homozygote" - SINGLE_HETEROZYGOTE = "SingleHeterozygote" - COMPOUND_HETEROZYGOTE = "CompoundHeterozygote" - HEMIZYGOTE = "Hemizygote" - NOT_PROVIDED = "not provided" - - -@enum.unique -class RelativeOrientation(enum.Enum): - """Relative orientation of two variants""" - - CIS = "cis" - TRANS = "trans" - UNKNOWN = "unknown" - - -class AlleleDescription(BaseModel): - """Description of one allele for use in co-occurence description""" - - model_config = ConfigDict(frozen=True) - - #: Name of the allele - name: str - #: Relative orientation in variant co-occurence - relative_orientation: typing.Optional[RelativeOrientation] - #: Zygosity information - zygosity: typing.Optional[Zygosity] = None - #: Clinical significance description of variant - clinical_significance: typing.Optional[ClinicalSignificanceRCV] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "AlleleDescription": - return AlleleDescription( - name=json_data["Name"], - relative_orientation=( - RelativeOrientation(json_data["RelativeOrientation"]) - if "RelativeOrientation" in json_data - else None - ), - zygosity=Zygosity(json_data["Zygosity"]) if "Zygosity" in json_data else None, - clinical_significance=( - ClinicalSignificanceRCV.from_json_data(json_data["ClinicalSignificance"]) - if "ClinicalSignificance" in json_data - else None - ), - ) - - -class Cooccurrence(BaseModel): - """Describes co-ocurrence of variants""" - - model_config = ConfigDict(frozen=True) - - #: The overall zygosity - zygosity: typing.Optional[Zygosity] = None - #: The description of the alleles - allele_descriptions: typing.List[AlleleDescription] = [] - #: A count (undocumented in ClinVar XML) - count: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Cooccurrence": - return Cooccurrence( - zygosity=Zygosity(json_data["Zygosity"]) if "Zygosity" in json_data else None, - allele_descriptions=[ - AlleleDescription.from_json_data(raw_allele_description) - for raw_allele_description in force_list(json_data.get("AlleleDescSet", [])) - ], - count=int(json_data["Count"]) if "Count" in json_data else None, - ) - - -@enum.unique -class ObservationMethod(enum.Enum): - """Method for generating an observation""" - - CURATION = "curation" - LITERATURE_ONLY = "literature only" - REFERENCE_POPULATION = "reference population" - RE_INTERPRETATION = "re-interpretation" - CASE_CONTROL = "case-control" - CLINICAL_TESTING = "clinical testing" - IN_VITRO = "in vitro" - IN_VIVO = "in vivo" - INFERRED_FROM_SOURCE = "inferred from source" - RESEARCH = "research" - NOT_PROVIDED = "not provided" - OTHER = "other" - - @classmethod - def from_the_wild(cls, str) -> "ObservationMethod": - """Convert values "from the wild" where sometimes invalid values are used. - - These are converted to ``Other``. - """ - try: - return ObservationMethod(str) - except ValueError: - return cls.OTHER - - -@enum.unique -class ObservedDataAttributeType(enum.Enum): - """Type for an attribute in a ``ObservedData``""" - - DESCRIPTION = "Description" - VARIANT_ALLELES = "VariantAlleles" - SUBJECTS_WITH_VARIANT = "SubjectsWithVariant" - SUBJECTS_WITH_DIFFERENT_CAUSATIVE_VARIANT = "SubjectsWithDifferentCausativeVariant" - VARIANT_CHROMOSOMES = "VariantChromosomes" - INDEPENDENT_OBSERVATIONS = "IndependentObservations" - SINGLE_HETEROZYGOTE = "SingleHeterozygote" - COMPOUND_HETEROZYGOTE = "CompoundHeterozygote" - HOMOZYGOTE = "Homozygote" - HEMIZYGOTE = "Hemizygote" - NUMBER_MOSAIC = "NumberMosaic" - OBSERVED_UNSPECIFIED = "ObservedUnspecified" - ALLELE_FREQUENCY = "AlleleFrequency" - SECONDARY_FINDING = "SecondaryFinding" - GENOTYPE_AND_MOI_CONSISTENT = "GenotypeAndMOIConsistent" - UNAFFECTED_FAMILY_MEMBER_WITH_CAUSATIVE_VARIANT = "UnaffectedFamilyMemberWithCausativeVariant" - HET_PARENT_TRANSMIT_NORMAL_ALLELE = "HetParentTransmitNormalAllele" - COSEGREGATING_FAMILY = "CosegregatingFamilies" - INFORMATIVE_MEIOSES = "InformativeMeioses" - SAMPLE_LOCAL_ID = "SampleLocalID" - SAMPLE_VARIANT_ID = "SampleVariantID" - FAMILY_HISTORY = "FamilyHistory" - NUM_FAMILIES_WITH_VARIANT = "NumFamiliesWithVariant" - NUM_FAMILIES_WITH_SEGREGATION_OBSERVED = "NumFamiliesWithSegregationObserved" - SEGREGATION_OBSERVED = "SegregationObserved" - - -class ObservedDataAttribute(BaseModel): - """Attribute for ``ObservedData``""" - - model_config = ConfigDict(frozen=True) - - #: The type of the attribute - type: ObservedDataAttributeType - #: The attribute's value - value: typing.Optional[str] = None - #: The optional integer value provided in ClinVar public XML - integer_value: typing.Optional[int] = None - #: The optional date value provided in ClinVar public XML - date_value: typing.Optional[datetime.date] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ObservedDataAttribute": - return ObservedDataAttribute( - type=ObservedDataAttributeType(json_data["@Type"]), - value=json_data.get("#text"), - integer_value=int(json_data["@integerValue"]) if "@integerValue" in json_data else None, - date_value=( - parse_datetime(json_data["@dateValue"]) if "@dateValue" in json_data else None - ), - ) - - -@enum.unique -class Severity(enum.Enum): - """Severity of a condition""" - - MILD = "mild" - MODERATE = "moderate" - SEVERE = "severe" - - -class ObservedData(BaseModel): - """Store structured observed data""" - - model_config = ConfigDict(frozen=True) - - #: The core observation data - attribute: ObservedDataAttribute - #: Optional description of severity - severity: typing.Optional[Severity] = None - #: Optional list of citations - citations: typing.List[Citation] = [] - #: Optional list of cross-references - xrefs: typing.List[Xref] = [] - #: Optional list of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ObservedData": - return ObservedData( - attribute=ObservedDataAttribute.from_json_data(json_data["Attribute"]), - severity=Severity(json_data["Severity"]) if "Severity" in json_data else None, - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -class SampleDescription(BaseModel): - """Description of a sample with optional citation""" - - model_config = ConfigDict(frozen=True) - - #: The sample's description - description: typing.Optional[Comment] = None - #: A citation for the sample - citation: typing.Optional[Citation] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "SampleDescription": - return SampleDescription( - description=( - Comment.from_json_data(json_data["Description"]) - if "Description" in json_data - else None - ), - citation=( - Citation.from_json_data(json_data["Citation"]) if "Citation" in json_data else None - ), - ) - - -class FamilyInfo(BaseModel): - """Description of a family in an observation. - - If the details of the number of families and the de-identified pedigree id are not available, - use FamilyHistory to describe what type of family data is available. Can also be used to report - 'Yes' or 'No' if there are no more details. - """ - - model_config = ConfigDict(frozen=True) - - #: Family history description - family_history: typing.Optional[str] = None - #: Number of families with observations - num_families: typing.Optional[int] = None - #: Number of families with a varaint - num_families_with_variant: typing.Optional[int] = None - #: Number of families with observed segregation - num_families_with_segregation_observed: typing.Optional[int] = None - #: Pedigree identifier - pedigree_id: typing.Optional[str] = None - #: Whether segration was observeds - segregation_observed: typing.Optional[bool] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "FamilyInfo": - return FamilyInfo( - family_history=json_data.get("FamilyHistory"), - num_families=int(json_data["@NumFamilies"]) if "@NumFamilies" in json_data else None, - num_families_with_variant=( - int(json_data["@NumFamiliesWithVariant"]) - if "@NumFamiliesWithVariant" in json_data - else None - ), - num_families_with_segregation_observed=( - int(json_data["@NumFamiliesWithSegregationObserved"]) - if "@NumFamiliesWithSegregationObserved" in json_data - else None - ), - pedigree_id=json_data.get("@PedigreeID"), - segregation_observed=( - json_data["@SegregationObserved"] == "yes" - if "@SegregationObserved" in json_data - else None - ), - ) - - -@enum.unique -class SampleOrigin(enum.Enum): - """Origin of a sample""" - - GERMLINE = "germline" - SOMATIC = "somatic" - DE_NOVO = "de novo" - UNKNOWN = "unknown" - NOT_PROVIDED = "not provided" - INHERITED = "inherited" - MATERNAL = "maternal" - PATERNAL = "paternal" - BIPARENTAL = "biparental" - NOT_REPORTED = "not reported" - TESTED_INCONCLUSIVE = "tested inconclusive" - NOT_APPLICABLE = "not applicable" - EXPERIMENTALLY_GENERATED = "experimentally generated" - - @classmethod - def from_the_wild(cls, s: str) -> "SampleOrigin": - """Convert values "from the wild" where sometimes invalid values are used. - - These are converted to ``Other``. - """ - try: - return SampleOrigin(s.replace("-", " ").lower()) - except ValueError: - return SampleOrigin.UNKNOWN - - -class Species(BaseModel): - """Definition of the species of a sample""" - - model_config = ConfigDict(frozen=True) - - #: The species name - value: str - #: The taxonomy id - taxonomy_id: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: typing.Union[dict, str]) -> "Species": - if isinstance(json_data, str): - return Species( - value=json_data, - ) - else: - return Species( - value=json_data["#text"], - taxonomy_id=int(json_data["@TaxonomyId"]), - ) - - -@enum.unique -class AgeType(enum.Enum): - """Type of an age or side of an age range""" - - MINIMUM = "minimum" - MAXIMUM = "maximum" - SINGLE = "single" - - -class Age(BaseModel): - """Description of an age or a side of an age range""" - - model_config = ConfigDict(frozen=True) - - #: The unit of the age - age_unit: str - #: The age value - value: int - #: The type of the age (side of a range or single age) - type: AgeType - - @classmethod - def from_json_data(cls, json_data: dict) -> "Age": - return Age( - age_unit=json_data["@age_unit"], - value=int(json_data["#text"]), - type=AgeType(json_data["@Type"]), - ) - - -@enum.unique -class AffectedStatus(enum.Enum): - """Affected status of a sample""" - - YES = "yes" - NO = "no" - NOT_PROVIDED = "not provided" - UNKNOWN = "unknown" - NOT_APPLICABLE = "not applicable" - - -@enum.unique -class Gender(enum.Enum): - """Gender of a sample""" - - MALE = "male" - FEMALE = "female" - MIXED = "mixed" - - -@enum.unique -class SampleSource(enum.Enum): - """Source of a sample""" - - SUBMITTER_GENERATED = "submitter generated" - DATA_MINING = "data mining" - - -class TypedValue(BaseModel): - """A typed value in a value set""" - - model_config = ConfigDict(frozen=True) - - #: The type description - type: str - #: The value - value: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "TypedValue": - return TypedValue( - type=json_data["@Type"], - value=json_data.get("#text"), - ) - - -class AnnotatedTypedValue(BaseModel): - """A further annotated ``TypedValue``""" - - model_config = ConfigDict(frozen=True) - - #: The inner typed value - value: TypedValue - #: Optional list of citations - citations: typing.List[Citation] = [] - #: Optional list of cross-references - xrefs: typing.List[Xref] = [] - #: Optional list of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "AnnotatedTypedValue": - if "ElementValue" in json_data: - value = TypedValue.from_json_data(json_data["ElementValue"]) - elif "Attribute" in json_data: - value = TypedValue.from_json_data(json_data["Attribute"]) - else: - raise TypeError(f"Expected ElementValue or Attribute in {json_data}") - return AnnotatedTypedValue( - value=value, - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class ClinicalFeaturesAffectedStatus(enum.Enum): - """Affected status of a clinical feature""" - - PRESENT = "present" - ABSENT = "absent" - NOT_TESTED = "not tested" - - -@enum.unique -class SourceType(enum.Enum): - """Type of a source""" - - LABORATORY = "laboratory" - LSDB = "locus-specific database (LSDB)" - CONSORTIUM = "consortium" - RESOURCE = "resource" - PATIENT_REGISTRY = "patient registry" - OTHER = "other" - - -class Source(BaseModel): - """Source information of some data""" - - model_config = ConfigDict(frozen=True) - - #: A standard term for the source of the information - data_source: str - #: The identifier used by the data source - id: typing.Optional[str] = None - #: Controlled terms to categorize the source of the information - source_type: typing.Optional[SourceType] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Source": - return Source( - data_source=json_data["@DataSource"], - id=json_data.get("@ID"), - source_type=( - SourceType(json_data["@SourceType"]) if json_data.get("@SourceType") else None - ), - ) - - -@enum.unique -class TraitRelationshipType(enum.Enum): - """Type of a trait relationship""" - - PHENOCOPY = "phenocopy" - SUBPHENOTYPE = "Subphenotype" - DRUG_RESPONSE_AND_DIASEASE = "DrugResponseAndDisease" - CO_OCCURRING_CONDITION = "co-occurring condition" - FINDING_MEMBER = "Finding member" - - -class TraitRelationship(BaseModel): - """Describe relations between two types""" - - model_config = ConfigDict(frozen=True) - - #: The type of the relationship - type: TraitRelationshipType - #: An optional identifier of the relationship - id: typing.Optional[int] = None - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - source: typing.List[Source] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "TraitRelationship": - return TraitRelationship( - type=TraitRelationshipType(json_data["@Type"]), - id=int(json_data["@ID"]) if "@ID" in json_data else None, - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - source=[ - Source.from_json_data(raw_source) - for raw_source in force_list(json_data.get("Source", [])) - ], - ) - - -class ClinVarAssertionTraitRelationship(BaseModel): - """Trait relationship for ``ClinVarAssertionTrait`` records""" - - model_config = ConfigDict(frozen=True) - - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: List of sources - sources: typing.List[Source] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionTraitRelationship": - return ClinVarAssertionTraitRelationship( - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - sources=[ - Source.from_json_data(raw_source) - for raw_source in force_list(json_data.get("Source", [])) - ], - ) - - -class ClinVarAssertionTrait(BaseModel): - """Trait description for a ClinVar assertion""" - - model_config = ConfigDict(frozen=True) - - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of trait relationships - trait_relationships: typing.List[TraitRelationship] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: List of sources - sources: typing.List[Source] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionTrait": - return ClinVarAssertionTrait( - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - trait_relationships=[ - TraitRelationship.from_json_data(raw_trait_relationship) - for raw_trait_relationship in force_list(json_data.get("TraitRelationship", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - sources=[ - Source.from_json_data(raw_source) - for raw_source in force_list(json_data.get("Source", [])) - ], - ) - - -@enum.unique -class TraitType(enum.Enum): - """Type of a trait""" - - DISEASE = "Disease" - DRUG_RESPONSE = "DrugResponse" - BLOOD_GROUP = "BloodGroup" - FINDING = "Finding" - NAMED_PROTEIN_VARIANT = "NamedProteinVariant" - PHENOTYPE_INSTRUCTION = "PhenotypeInstruction" - - -class Trait(BaseModel): - """Trait description for trait sets""" - - model_config = ConfigDict(frozen=True) - - #: Type of the trait - type: TraitType - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of trait relationships - trait_relationships: typing.List[TraitRelationship] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: List of sources - sources: typing.List[Source] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "Trait": - return Trait( - type=TraitType(json_data["@Type"]), - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - trait_relationships=[ - TraitRelationship.from_json_data(raw_trait_relationship) - for raw_trait_relationship in force_list(json_data.get("TraitRelationship", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - sources=[ - Source.from_json_data(raw_source) - for raw_source in force_list(json_data.get("Source", [])) - ], - ) - - -@enum.unique -class IndicationType(enum.Enum): - """Type of an indication""" - - INDICATION = "Indication" - - -class Indication(BaseModel): - """Connect trait to test""" - - model_config = ConfigDict(frozen=True) - - #: List of traits - traits: typing.List[ClinVarAssertionTrait] = [] - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comment: typing.Optional[Comment] = None - #: The type of the indication - type: typing.Optional[IndicationType] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Indication": - return Indication( - type=IndicationType(json_data["@Type"]), - traits=[ - ClinVarAssertionTrait.from_json_data(raw_trait) - for raw_trait in force_list(json_data.get("Trait", [])) - ], - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("Attribute", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comment=( - Comment.from_json_data(json_data["Comment"]) if "Comment" in json_data else None - ), - ) - - -class Sample(BaseModel): - """A sample from a ClinVar XML file""" - - model_config = ConfigDict(frozen=True) - - #: Sample description - description: typing.Optional[SampleDescription] = None - #: Sample origin - origin: typing.Optional[SampleOrigin] = None - #: Proband's ethnicity - ethnicity: typing.Optional[str] = None - #: Geographic origin - geographic_origin: typing.Optional[str] = None - #: Tissue - tissue: typing.Optional[str] = None - #: Cell line - cell_line: typing.Optional[str] = None - #: Species - species: typing.Optional[Species] = None - #: Age - age: typing.List[Age] = [] - #: Strain - strain: typing.Optional[str] = None - #: Affected status - affected_status: AffectedStatus = AffectedStatus.NOT_PROVIDED - #: Denominator, total individuals included in this observation set. - number_tested: typing.Optional[int] = None - #: Denominator, total males included in this observation set. - number_males: typing.Optional[int] = None - #: Denominator, total females included in this observation set. - number_females: typing.Optional[int] = None - #: Denominator, total number chromosomes tested. Number affected and - #: unaffected are captured in the element NumberObserved. - number_chr_tested: typing.Optional[int] = None - #: Gender should be used ONLY if explicit values are not available for number - #: of males or females, and there is a need to indicate that the genders in - #: the sample are known. - gender: typing.Optional[Gender] = None - #: Family data - family_data: typing.Optional[FamilyInfo] = None - #: Proband - proband: typing.Optional[str] = None - #: Indication - indication: typing.Optional[Indication] = None - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: Sample source - source: typing.Optional[SampleSource] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Sample": - origin = None - if "Origin" in json_data: - raw_origin = extract_text(json_data["Origin"]) - if raw_origin: - origin = SampleOrigin.from_the_wild(raw_origin) - return Sample( - description=( - SampleDescription.from_json_data(json_data["SampleDescription"]) - if "SampleDescription" in json_data - else None - ), - origin=origin, - ethnicity=json_data.get("Ethnicity"), - geographic_origin=json_data.get("GeographicOrigin"), - tissue=extract_text(json_data["Tissue"]) if "Tissue" in json_data else None, - cell_line=json_data["CellLine"] if "CellLine" in json_data else None, - species=( - Species.from_json_data(json_data["Species"]) - if ("Species" in json_data and json_data.get("Species")) - else None - ), - age=[Age.from_json_data(raw_age) for raw_age in force_list(json_data.get("Age", []))], - strain=json_data.get("Strain"), - affected_status=( - AffectedStatus(extract_text(json_data["AffectedStatus"])) - if "AffectedStatus" in json_data - else AffectedStatus.NOT_PROVIDED - ), - number_tested=( - int(extract_text(json_data["NumberTested"]) or 0) - if "NumberTested" in json_data - else None - ), - number_males=( - int(extract_text(json_data["NumberMales"]) or 0) - if "NumberMales" in json_data - else None - ), - number_females=( - int(extract_text(json_data["NumberFemales"]) or 0) - if "NumberFemales" in json_data - else None - ), - number_chr_tested=( - int(extract_text(json_data["NumberChrTested"]) or 0) - if "NumberChrTested" in json_data - else None - ), - gender=Gender(extract_text(json_data["Gender"])) if "Gender" in json_data else None, - family_data=( - FamilyInfo.from_json_data(json_data["FamilyData"]) - if "FamilyData" in json_data - else None - ), - proband=json_data.get("Proband"), - indication=( - Indication.from_json_data(json_data["Indication"]) - if "Indication" in json_data - else None - ), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - source=SampleSource(json_data["SourceType"]) if "SourceType" in json_data else None, - ) - - -@enum.unique -class TraitSetType(enum.Enum): - """Type of a trait set""" - - DISEASE = "Disease" - DRUG_RESPONSE = "DrugResponse" - FINDING = "Finding" - PHENOTYPE_INSTRUCTION = "PhenotypeInstruction" - TRAIT_CHOICE = "TraitChoice" - - -class TraitSet(BaseModel): - """Description of a trait set""" - - model_config = ConfigDict(frozen=True) - - #: Type of the trait set - type: TraitSetType - #: List of traits - traits: typing.List[Trait] = [] - #: Optional identifier - id: typing.Optional[int] = None - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[AnnotatedTypedValue] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "TraitSet": - return cls( - type=TraitSetType(json_data["@Type"]), - traits=[ - Trait.from_json_data(raw_trait) - for raw_trait in force_list(json_data.get("Trait", [])) - ], - id=int(json_data["@ID"]) if json_data.get("@ID") else None, - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - AnnotatedTypedValue.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -class ObservationSet(BaseModel): - """Documents in what populations or samples an allele or genotype has been observed - relative to the described trait. - - Summary observations can be registered per submitted assertion, grouped by common - citation, study type, origin, ethnicity, tissue, cell line, and species data. Not - all options are valid per study type, but these will not be validated in the xsd. - """ - - model_config = ConfigDict(frozen=True) - - #: Sample in observation - sample: Sample - #: List of observation methods - methods: typing.List[ObservationMethod] = [] - #: List of observed data - observed_data: typing.List[ObservedData] = [] - #: Traits - traits: typing.Optional[TraitSet] = None - #: List of co-occurrences - cooccurrences: typing.List[Cooccurrence] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ObservationSet": - return ObservationSet( - sample=Sample.from_json_data(json_data["Sample"]), - methods=[ - ObservationMethod.from_the_wild(method["MethodType"]) - for method in force_list(json_data.get("Method", [])) - ], - observed_data=[ - ObservedData.from_json_data(raw_observed_data) - for raw_observed_data in force_list(json_data.get("ObservedData", [])) - ], - traits=( - TraitSet.from_json_data(json_data["TraitSet"]) if "TraitSet" in json_data else None - ), - cooccurrences=[ - Cooccurrence.from_json_data(raw_cooccurrence) - for raw_cooccurrence in force_list(json_data.get("Coocurrence", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class AssertionType(enum.Enum): - """The assertion types for RCV records""" - - VARIATION_TO_DISEASE = "variation to disease" - VARIATION_IN_MODIFIER_GENE_TO_DISEASE = "variation in modifier gene to disease" - CONFERS_SENSITIVITY = "confers sensitivity" - CONFERS_RESISTANCE = "confers resistance" - VARIANT_TO_NAMED_PROTEIN_EFFECT = "variant to named protein" - - -@enum.unique -class MeasureSetAttributeType(enum.Enum): - """Type of an attribute in a measure set""" - - DESCRIPTION = "Description" - MOLECULAR_CONSEQUENCE = "MolecularConsequence" - HGVS = "HGVS" - HGVS_GENOMIC_TOP_LEVEL = "HGVS, genomic, top level" - HGVS_GENOMIC_TOP_LEVEL_PREVIOUS = "HGVS, genomic, top level, previous" - HGVS_GENOMIC_TOP_LEVEL_OTHER = "HGVS, genomic, top level, other" - HGVS_GENOMIC_REFSEQGENE = "HGVS, genomic, RefSeqGene" - HGVS_GENOMIC_LRG = "HGVS, genomic, LRG" - HGVS_CODING_REFSEQGENE = "HGVS, coding, RefSeq" - HGVS_CODING_LRG = "HGVS, coding, LRG" - HGVS_CODING = "HGVS, coding" - HGVS_RNA = "HGVS, RNA" - HGVS_PREVIOUS = "HGVS, previous" - HGVS_PROTEIN = "HGVS, protein" - HGVS_PROTEIN_REFSEQ = "HGVS, protein, RefSeq" - HGVS_NUCLEOTIDE = "HGVS, nucleotide" - HGVS_NON_VALIDATED = "HGVS, non-validated" - HGVS_LEGACY = "HGVS, legacy" - HGVS_UNCERTAIN = "HGVS, uncertain" - FUNCTIONAL_CONSEQUENCE = "FunctionalConsequence" - ISCN_COORDINATES = "ISCNCoordinates" - SUBMITTER_VARIANT_ID = "SubmitterVariantId" - - -class MeasureSetAttribute(BaseModel): - """An attribute in a MeasureSet""" - - model_config = ConfigDict(frozen=True) - - #: Type of the attribute - type: MeasureSetAttributeType - #: Value of the attribute - value: str - #: Described change - change: typing.Optional[str] = None - #: Whether the attribute is MANE select - mane_select: typing.Optional[bool] = None - #: Whether the attribute is in MANE plus clinical - mane_plus_clinical: typing.Optional[bool] = None - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "MeasureSetAttribute": - attribute = json_data["Attribute"] - return MeasureSetAttribute( - type=MeasureSetAttributeType(attribute["@Type"]), - value=attribute["#text"], - change=attribute.get("@Change"), - mane_select=attribute["@ManeSelect"] == "yes" if "@ManeSelect" in attribute else None, - mane_plus_clinical=( - attribute["@ManePlusClinical"] == "yes" - if "@ManePlusClinical" in attribute - else None - ), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class MeasureAttributeType(enum.Enum): - """Type of an attribute in a measure type""" - - HGVS_GENOMIC_TOP_LEVEL = "HGVS, genomic, top level" - HGVS_GENOMIC_TOP_LEVEL_PREVIOUS = "HGVS, genomic, top level, previous" - HGVS_GENOMIC_TOP_LEVEL_OTHER = "HGVS, genomic, top level, other" - HGVS_GENOMIC_REFSEQGENE = "HGVS, genomic, RefSeqGene" - HGVS_GENOMIC_LRG = "HGVS, genomic, LRG" - HGVS_GENOMIC = "HGVS, genomic" - HGVS_CODING_REFSEQGENE = "HGVS, coding, RefSeq" - HGVS_CODING_LRG = "HGVS, coding, LRG" - HGVS_CODING = "HGVS, coding" - HGVS_INCOMPLETE = "HGVS, incomplete" - HGVS_PREVIOUS = "HGVS, previous" - HGVS_PROTEIN = "HGVS, protein" - HGVS_PROTEIN_REFSEQ = "HGVS, protein, RefSeq" - HGVS_NON_CODING = "HGVS, non-coding" - HGVS_NON_VALIDATED = "HGVS, non-validated" - HGVS_RNA = "HGVS, RNA" - HGVS_LEGACY = "HGVS, legacy" - HGVS_UNCERTAIN = "HGVS, uncertain" - HGVS = "HGVS" - NON_HGVS = "NonHGVS" - LOCATION = "Location" - MISCELLANEOUS_DESCRIPTION = "MiscellaneousDescription" - DESCRIPTION = "Description" - FUNCTIONAL_CONCESEQUENCE = "FunctionalConsequence" - MOLECULAR_CONSEQUENCE = "MolecularConsequence" - PROTEIN_CHANGE_1_LETTER_CODE = "ProteinChange1LetterCode" - PROTEIN_CHANGE_3_LETTER_CODE = "ProteinChange3LetterCode" - ACTIVITY_LEVEL = "ActivityLevel" - SUSPECT = "Suspect" - ALLELIC_VARIANT_PREVIOUS = "Allelic Variant, previous" - ACCEPTOR_SPLICE_SITE = "acceptor splice site" - DONOR_SPLICE_SITE = "donor splice site" - NUCLEOTIDE_CHANGE = "nucleotide change" - PROTEIN_CHANGE_HISTORICAL = "protein change, historical" - TRANSCRIPT_VARIANT = "transcript variant" - ABSOLUTE_COPY_NUMBER = "AbsoluteCopyNumber" - REFERENCE_COPY_NUMBER = "ReferenceCopyNumber" - COPY_NUMBER_TUPLE = "CopyNumberTuple" - COSMIC = "COSMIC" - SUBMITTER_VARIANT_ID = "SubmitterVariantId" - ISCN_COORDINATES = "ISCNCoordinates" - - -class MeasureAttribute(BaseModel): - """An attribute in a MeasureType""" - - model_config = ConfigDict(frozen=True) - - #: The type of the attribute - type: MeasureAttributeType - #: Value of the attribute - value: typing.Optional[str] = None - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: The optional integer value provided in ClinVar public XML - integer_value: typing.Optional[int] = None - #: The optional date value provided in ClinVar public XML - date_value: typing.Optional[datetime.date] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "MeasureAttribute": - attribute = json_data["Attribute"] - return MeasureAttribute( - type=MeasureAttributeType(attribute["@Type"]), - value=attribute.get("#text"), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - integer_value=int(attribute["@integerValue"]) if "@integerValue" in attribute else None, - date_value=( - parse_datetime(attribute["@dateValue"]) if "@dateValue" in attribute else None - ), - ) - - -class AlleleFrequency(BaseModel): - """Description of an allele frequency""" - - model_config = ConfigDict(frozen=True) - - #: AF value - value: float - #: AF source - source: str - #: URL - url: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "AlleleFrequency": - return AlleleFrequency( - value=float(json_data["@Value"]), - source=json_data["@Source"], - url=json_data.get("@URL"), - ) - - -class GlobalMinorAlleleFrequency(BaseModel): - """Description of a global minor allele frequency""" - - model_config = ConfigDict(frozen=True) - - #: MAF value - value: float - #: MAF source - source: str - #: Minor allele string - minor_allele: typing.Optional[str] = None - #: URL - url: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "GlobalMinorAlleleFrequency": - return GlobalMinorAlleleFrequency( - value=float(json_data["@Value"]), - source=json_data["@Source"], - minor_allele=json_data.get("@MinorAllele"), - url=json_data.get("@URL"), - ) - - -@enum.unique -class AssemblyStatus(enum.Enum): - """Status of an assembly""" - - CURRENT = "current" - PREVIOUS = "previous" - - -class SequenceLocation(BaseModel): - """Description of a location on a sequence""" - - model_config = ConfigDict(frozen=True) - - #: Assembly of the location - assembly: str - #: Chromosome - chr: str - #: Accession - accession: typing.Optional[str] = None - #: Outer start position (1-based) - outer_start: typing.Optional[int] = None - #: Inner start position (1-based) - inner_start: typing.Optional[int] = None - #: Start position (1-based) - start: typing.Optional[int] = None - #: Stop position (1-based) - stop: typing.Optional[int] = None - #: Inner stop position (1-based) - inner_stop: typing.Optional[int] = None - #: Outer stop position (1-based) - outer_stop: typing.Optional[int] = None - #: Display start position (1-based) - display_start: typing.Optional[int] = None - #: Display stop position (1-based) - display_stop: typing.Optional[int] = None - #: Strand - strand: typing.Optional[str] = None - #: Variant length - variant_length: typing.Optional[int] = None - #: Reference allele - reference_allele: typing.Optional[str] = None - #: Alternate allele - alternate_allele: typing.Optional[str] = None - #: Assembly accession and version - assembly_accession_version: typing.Optional[str] = None - #: Assembly status - assembly_status: typing.Optional[AssemblyStatus] = None - #: Position in VCF - position_vcf: typing.Optional[int] = None - #: Reference allele in VCF - reference_allele_vcf: typing.Optional[str] = None - #: Alternate allele in VCF - alternate_allele_vcf: typing.Optional[str] = None - #: Whether the location is for display length - for_display_length: typing.Optional[bool] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "SequenceLocation": - return SequenceLocation( - assembly=json_data["@Assembly"], - chr=json_data["@Chr"], - accession=json_data.get("@Accession"), - outer_start=int(json_data["@outerStart"]) if "@outerStart" in json_data else None, - inner_start=int(json_data["@innerStart"]) if "@innerStart" in json_data else None, - start=int(json_data["@start"]) if "@start" in json_data else None, - stop=int(json_data["@stop"]) if "@stop" in json_data else None, - inner_stop=int(json_data["@innerStop"]) if "@innerStop" in json_data else None, - outer_stop=int(json_data["@outerStop"]) if "@outerStop" in json_data else None, - display_start=( - int(json_data["@display_start"]) if "@display_start" in json_data else None - ), - display_stop=int(json_data["@display_stop"]) if "@display_stop" in json_data else None, - strand=json_data.get("@Strand"), - variant_length=( - int(json_data["@variantLength"]) if "@variantLength" in json_data else None - ), - reference_allele=json_data.get("@referenceAllele"), - alternate_allele=json_data.get("@alternateAllele"), - assembly_accession_version=json_data.get("@AssemblyAccessionVersion"), - assembly_status=( - AssemblyStatus(json_data["@AssemblyStatus"]) - if "@AssemblyStatus" in json_data - else None - ), - position_vcf=int(json_data["@positionVCF"]) if "@positionVCF" in json_data else None, - reference_allele_vcf=json_data.get("@referenceAlleleVCF"), - alternate_allele_vcf=json_data.get("@alternateAlleleVCF"), - for_display_length=( - json_data["@forDisplayLength"] == "true" - if "@forDisplayLength" in json_data - else None - ), - ) - - -@enum.unique -class MeasureRelationshipAttributeType(enum.Enum): - """Type of an attribute in ``MeasureRelationship``""" - - HGVS = "HGVS" - GENOTYPE = "genotype" - HAPLOINSUFFICIENCY = "Haploinsufficiency" - TRIPLOSENSITIVITY = "Triplosensitivity" - GENE_RELATIONSHIPS = "gene relationships" - - -class MeasureRelationshipAttribute(BaseModel): - """Attribute of a measure releationship""" - - model_config = ConfigDict(frozen=True) - - #: The attribute's value - value: str - #: The attribute's type - type: MeasureRelationshipAttributeType - #: The optional integer value provided in ClinVar public XML - integer_value: typing.Optional[int] = None - #: The optional date value provided in ClinVar public XML - date_value: typing.Optional[datetime.date] = None - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "MeasureRelationshipAttribute": - attribute = json_data["Attribute"] - return MeasureRelationshipAttribute( - # value of tag - value=attribute["#text"], - type=MeasureRelationshipAttributeType(attribute["@Type"]), - integer_value=int(attribute["@integerValue"]) if "@integerValue" in attribute else None, - date_value=( - parse_datetime(attribute["@dateValue"]) if "@dateValue" in attribute else None - ), - # other data in lists - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class MeasureRelationshipType(enum.Enum): - VARIANT_IN_GENE = "variant in gene" - COOCURRING_VARIANT = "co-occurring variant" - WITHIN_SNIGLE_GENE = "within single gene" - WITHIN_MULTIPLE_GENES_BY_OVERLAP = "within multiple genes by overlap" - GENES_OVERLAPPED_BY_VARIANT = "genes overlapped by variant" - NEAR_GENE_UPSTREAM = "near gene, upstream" - NEAR_GENE_DOWNSTREAM = "near gene, downstream" - ASSERTED_BUT_NOT_COMPUTED = "asserted, but not computed" - - -class MeasureRelationship(BaseModel): - """Description of a measure relationship""" - - model_config = ConfigDict(frozen=True) - - #: Type of the measure relationship - type: typing.Optional[MeasureRelationshipType] = None - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[MeasureRelationshipAttribute] = [] - #: Sequence locations - sequence_locations: typing.List[SequenceLocation] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "MeasureRelationship": - return MeasureRelationship( - type=MeasureRelationshipType(json_data["@Type"]) if "@Type" in json_data else None, - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - MeasureRelationshipAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("Attribute", [])) - ], - sequence_locations=[ - SequenceLocation.from_json_data(raw_sequence_location) - for raw_sequence_location in force_list(json_data.get("SequenceLocation", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class MeasureType(enum.Enum): - GENE = "gene" - VARIATION = "variation" - INSERTION = "insertion" - DELETION = "deletion" - SNV = "single nucleotide variant" - INDEL = "indel" - DUPLICATION = "duplication" - TANDEM_DUPLICATION = "tandem duplication" - STRUCTURAL_VARIANT = "structural variant" - COPY_NUMBER_GAIN = "copy number gain" - COPY_NUMBER_LOSS = "copy number loss" - PROTEIN_ONLY = "protein only" - MICROSATELLITE = "microsatellite" - FUSION = "fusion" - INVERSION = "inversion" - TRANSLOCATION = "translocation" - QTL = "qtl" - COMPLEX = "complex" - OTHER = "other" - - @classmethod - def from_the_wild(cls, value: str) -> "MeasureType": - """Convert values "from the wild" where sometimes invalid values are used. - - These are converted to ``Other``. - """ - try: - return MeasureType(value.lower().replace("-", " ")) - except ValueError: - return MeasureType.OTHER - - -class Measure(BaseModel): - """Description of a measures""" - - model_config = ConfigDict(frozen=True) - - #: Type of the measure - type: typing.Optional[MeasureType] = None - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: Canonical SPDI - canonical_spdi: typing.Optional[str] = None - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[MeasureAttribute] = [] - #: List of allele frequencies - allele_frequencies: typing.List[AlleleFrequency] = [] - #: Global minor allele frequency - global_minor_allele_frequency: typing.Optional[GlobalMinorAlleleFrequency] = None - #: Cytogenic location - cytogenic_locations: typing.List[str] = [] - #: Sequence location - sequence_locations: typing.List[SequenceLocation] = [] - #: Measure relationship - measure_relationship: typing.List[MeasureRelationship] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: List of sources - source: typing.List[Source] = [] - #: Optional identifier - id: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Measure": - return Measure( - type=MeasureType.from_the_wild(json_data["@Type"]) if "@Type" in json_data else None, - id=int(json_data["@ID"]) if "@ID" in json_data else None, - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - canonical_spdi=json_data.get("CanonicalSPDI"), - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - MeasureAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - allele_frequencies=[ - AlleleFrequency.from_json_data(raw_allele_frequency) - for raw_allele_frequency in force_list(json_data.get("AlleleFrequency", [])) - ], - global_minor_allele_frequency=( - GlobalMinorAlleleFrequency.from_json_data(json_data["GlobalMinorAlleleFrequency"]) - if "GlobalMinorAlleleFrequency" in json_data - else None - ), - cytogenic_locations=[ - raw_cytogenic_location - for raw_cytogenic_location in force_list(json_data.get("CytogeneticLocation", [])) - ], - sequence_locations=[ - SequenceLocation.from_json_data(raw_sequence_location) - for raw_sequence_location in force_list(json_data.get("SequenceLocation", [])) - ], - measure_relationship=[ - MeasureRelationship.from_json_data(raw_measure_relationship) - for raw_measure_relationship in force_list(json_data.get("MeasureRelationship", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - source=[ - Source.from_json_data(raw_source) - for raw_source in force_list(json_data.get("Source", [])) - ], - ) - - -@enum.unique -class MeasureSetType(enum.Enum): - """Type of a measure set""" - - GENE = "Gene" - VARIANT = "Variant" - GENE_VARIANT = "gene-variant" - OMIM_RECORD = "OMIM record" - HAPLOTYPE = "Haplotype" - HAPLOTYPE_SINGLE_VARIANT = "Haplotype, single variant" - PHASE_UNKNOWN = "Phase unknown" - DISTINCT_CHROMOSOMES = "Distinct chromosomes" - COMPOUND_HETEROZYGOUS = "Compound heterozygous" - DIPLOTYPE = "Diplotype" - - -class MeasureSet(BaseModel): - """A collection of ``Measure`` objects with further annotations""" - - model_config = ConfigDict(frozen=True) - - #: Type of the measure - type: MeasureSetType - #: Accession of the measure - acc: typing.Optional[str] = None - #: Version of the measure - version: typing.Optional[int] = None - #: List of measures - measures: typing.List[Measure] = [] - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[MeasureSetAttribute] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: Number of chromosomes - number_of_chromosomes: typing.Optional[int] = None - #: Optional identifier - id: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "MeasureSet": - return MeasureSet( - type=MeasureSetType(json_data["@Type"]), - acc=json_data.get("@Acc"), - version=int(json_data["@Version"]) if json_data.get("@Version") else None, - measures=[ - Measure.from_json_data(raw_measure) - for raw_measure in force_list(json_data.get("Measure", [])) - ], - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - MeasureSetAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - number_of_chromosomes=( - int(json_data["@NumberOfChromosomes"]) - if json_data.get("@NumberOfChromosomes") - else None - ), - id=int(json_data["@ID"]) if json_data.get("@ID") else None, - ) - - -@enum.unique -class GenotypeSetType(enum.Enum): - """Type for a genotype set""" - - COMPOUND_HETEROZYGOTE = "CompoundHeterozygote" - DIPLOTYPE = "Diplotype" - - -class GenotypeSet(BaseModel): - """Genotype set description (compound heterozygote or diplotype)""" - - model_config = ConfigDict(frozen=True) - - #: Type of the genotype set - type: GenotypeSetType - #: List of measures - measures: typing.List[MeasureSet] = [] - #: List of names - names: typing.List[AnnotatedTypedValue] = [] - #: List of symbols - symbols: typing.List[AnnotatedTypedValue] = [] - #: List of attributes - attributes: typing.List[MeasureSetAttribute] = [] - #: List of citations - citations: typing.List[Citation] = [] - #: List of cross-references - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: Optional identifier - id: typing.Optional[int] = None - #: Optional accession - acc: typing.Optional[str] = None - #: Optional version - version: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "GenotypeSet": - return GenotypeSet( - type=GenotypeSetType(json_data["@Type"]), - measures=[ - MeasureSet.from_json_data(raw_measure) - for raw_measure in force_list(json_data.get("MeasureSet", [])) - ], - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - MeasureSetAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - id=int(json_data["@ID"]) if json_data.get("@ID") else None, - acc=json_data.get("@Acc"), - version=json_data.get("@Version"), - ) - - -class ReferenceClinVarAssertion(BaseModel): - """The reference ClinVar assertion""" - - model_config = ConfigDict(frozen=True) - - #: Accesion of the RCV record. - clinvar_accession: ReferenceClinVarAccession - #: Status of the record. - record_status: RecordStatus - #: Clinical significance summary of RCV record. - clinical_significance: ClinicalSignificanceRCV - #: The assertion RCV type. - assertion: AssertionType - #: Represents the public identifier a source may have for this record. - external_ids: typing.List[Xref] = [] - #: Attributes of the RCV record - attributes: typing.List[ReferenceClinVarAssertionAttribute] = [] - #: Observations. - observed_in: typing.List[ObservationSet] = [] - #: Measurement information, mutually exlusive with ``genotypes``. - measures: typing.Optional[MeasureSet] = None - #: Genotyping information, mutually exlusive with ``measures``. - genotypes: typing.Optional[GenotypeSet] = None - #: List of traits - traits: typing.Optional[TraitSet] = None - #: List of citations - citations: typing.List[Citation] = [] - #: List of comments - comments: typing.List[Comment] = [] - #: Date created - date_created: typing.Optional[datetime.date] = None - #: Date last updated - date_last_updated: typing.Optional[datetime.date] = None - #: Submission date - submission_date: typing.Optional[datetime.date] = None - #: Optional identifier - id: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ReferenceClinVarAssertion": - return ReferenceClinVarAssertion( - clinvar_accession=ReferenceClinVarAccession.from_json_data( - json_data["ClinVarAccession"] - ), - record_status=RecordStatus(json_data["RecordStatus"]), - clinical_significance=ClinicalSignificanceRCV.from_json_data( - json_data["ClinicalSignificance"] - ), - assertion=AssertionType(json_data["Assertion"]["@Type"]), - external_ids=[ - Xref.from_json_data(raw_external_id) - for raw_external_id in force_list(json_data.get("ExternalID", [])) - ], - attributes=[ - ReferenceClinVarAssertionAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("Attribute", [])) - ], - observed_in=[ - ObservationSet.from_json_data(raw_observations) - for raw_observations in force_list(json_data.get("ObservedIn", [])) - ], - measures=( - MeasureSet.from_json_data(json_data["MeasureSet"]) - if json_data.get("MeasureSet") - else None - ), - genotypes=( - GenotypeSet.from_json_data(json_data["GenotypeSet"]) - if json_data.get("GenotypeSet") - else None - ), - traits=( - TraitSet.from_json_data(json_data["TraitSet"]) if "TraitSet" in json_data else None - ), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - date_created=( - parse_datetime(json_data["@DateCreated"]).date() - if json_data.get("@DateCreated") - else None - ), - date_last_updated=( - parse_datetime(json_data["@DateLastUpdated"]).date() - if json_data.get("@DateLastUpdated") - else None - ), - submission_date=( - parse_datetime(json_data["@SubmissionDate"]).date() - if json_data.get("@SubmissionDate") - else None - ), - id=int(json_data["@ID"]) if json_data.get("@ID") else None, - ) - - -class ClinVarSubmissionId(BaseModel): - """Corresponds to ``ClinVarSubmissionID`` in XML file""" - - model_config = ConfigDict(frozen=True) - - #: Of primary use to submitters, to facilitate identification of records corresponding to - #: their submissions. If not provided by a submitter, NCBI generates. If provided by - #: submitter, that is represented in localKeyIsSubmitted. - local_key: str - #: Name of the submitter - submitter: typing.Optional[str] = None - #: Title of the submission - title: typing.Optional[str] = None - #: Assembly used in submission - submitted_assembly: typing.Optional[str] = None - #: Submission date - submitter_date: typing.Optional[datetime.date] = None - #: Whether the local key was submitted (True) or has ben set by NCBI (False) - local_key_is_submitted: typing.Optional[bool] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarSubmissionId": - return ClinVarSubmissionId( - local_key=json_data["@localKey"], - submitter=json_data.get("@submitter"), - title=json_data.get("@title"), - submitted_assembly=json_data.get("@submittedAssembly"), - submitter_date=( - parse_datetime(json_data["@submitterDate"] or "").date() - if json_data.get("@submitterDate") - else None - ), - local_key_is_submitted=( - json_data.get("localKeyIsSubmitted") == "1" - if json_data.get("localKeyIsSubmitted") - else None - ), - ) - - -@enum.unique -class SubmitterType(enum.Enum): - """Enumeration with ``Submitter.type``""" - - PRIMARY = "primary" - SECONDARY = "secondary" - BEHALF = "behalf" - - -class Submitter(BaseModel): - """A structure to support reportng the name of a submitter, its org_id, and whether primary - or secondary or behalf. - - Corresponds to ``SubmitterType`` in XML file. - """ - - model_config = ConfigDict(frozen=True) - - #: The type of the submitter - type: SubmitterType - #: The name of the submitter - submitter_name: typing.Optional[str] = None - #: The ID of the submitting organisation - org_id: typing.Optional[int] = None - #: The submitter category - category: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "Submitter": - return cls( - type=SubmitterType(json_data["@Type"]), - submitter_name=json_data.get("@SubmitterName"), - org_id=int(json_data["@OrgID"]) if "@OrgID" in json_data else None, - category=json_data.get("@Category"), - ) - - -@enum.unique -class ClinVarAssertionAccessionType(enum.Enum): - """ClinVar assertion accession type""" - - RCV = "RCV" - SCV = "SCV" - - -class ClinVarAssertionAccession(BaseModel): - """Accession number for a ClinVar record in a ``ClinVarAssertion``""" - - model_config = ConfigDict(frozen=True) - - #: The accession - acc: str - #: The version - version: int - #: The accession type - type: ClinVarAssertionAccessionType - #: The date that the latest update to the submitted record became public in ClinVar. - date_updated: typing.Optional[datetime.date] = None - #: DateCreated is the date when the record first became public in ClinVar. - date_created: typing.Optional[datetime.date] = None - #: The ID of the submitting organisation - org_id: typing.Optional[str] = None - #: The abbreviation of the submitting organisation - org_abbreviation: typing.Optional[str] = None - #: The type of the organisation - org_type: typing.Optional[str] = None - #: The category of the organisation. - org_category: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionAccession": - return ClinVarAssertionAccession( - acc=json_data["@Acc"], - version=int(json_data["@Version"]), - type=ClinVarAssertionAccessionType(json_data["@Type"]), - date_updated=( - parse_datetime(json_data["@DateUpdated"] or "").date() - if json_data.get("@DateUpdated") - else None - ), - date_created=( - parse_datetime(json_data["@DateCreated"] or "").date() - if json_data.get("@DateCreated") - else None - ), - org_id=json_data.get("@OrgID"), - org_abbreviation=json_data.get("@OrgAbbreviation"), - org_type=json_data.get("@OrgType"), - org_category=json_data.get("@OrganizationCategory"), - ) - - -class RecordHistory(BaseModel): - """A structure to support reporting of an accession, its version, the date its status - changed, and text describing that change. - """ - - model_config = ConfigDict(frozen=True) - - #: The accession - accession: str - #: The version - version: int - #: The date the status changed - date_changed: datetime.date - #: Comment text - comment: typing.Optional[str] = None - #: Attribute @VaritionID is only populated for VCV, where @Accession is like VCV000000009 - variation_id: typing.Optional[int] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "RecordHistory": - return cls( - accession=json_data["@Accession"], - version=int(json_data["@Version"]), - date_changed=parse_datetime(json_data["@DateChanged"]).date(), - comment=json_data.get("@Comment"), - variation_id=int(json_data["@VariationID"]) if json_data.get("@VariationID") else None, - ) - - -@enum.unique -class ClinVarAssertionAttributeType(enum.Enum): - MODE_OF_INHERITANCE = "ModeOfInheritance" - PENETRANCE = "Penetrance" - AGE_OF_ONSET = "AgeOfOnset" - SEVERITY = "Severity" - CLINICAL_SIGNIFICANCE_HISTORY = "ClinicalSignificanceHistory" - SEVERITY_DESCRIPTION = "SeverityDescription" - ASSERTION_METHOD = "AssertionMethod" - - -class ClinVarAssertionAttribute(BaseModel): - model_config = ConfigDict(frozen=True) - - type: ClinVarAssertionAttributeType - value: str - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionAttribute": - return cls( - type=ClinVarAssertionAttributeType(json_data["@Type"]), - value=json_data["#text"], - ) - - -class ClinVarAssertionAttributeSet(BaseModel): - """AttributeSet is a package to represent a unit of information, the source(s) of that unit, - identifiers representing that unit, and comments. - """ - - model_config = ConfigDict(frozen=True) - - #: Specification of the attribute set type. - attribute: ClinVarAssertionAttribute - #: List of citations - citations: typing.List[Citation] = [] - #: List of Xrefs - xrefs: typing.List[Xref] = [] - #: List of comments - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionAttributeSet": - return cls( - attribute=ClinVarAssertionAttribute.from_json_data(json_data["Attribute"]), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -class ClinAsserTraitSetTypeAttribute(BaseModel): - model_config = ConfigDict(frozen=True) - - value: str - type: str - citations: typing.List[Citation] = [] - xrefs: typing.List[Xref] = [] - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinAsserTraitSetTypeAttribute": - return cls( - value=json_data["#text"], - type=json_data["@Type"], - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - xrefs=[ - Xref.from_json_data(raw_xref) for raw_xref in force_list(json_data.get("XRef", [])) - ], - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -@enum.unique -class ClinVarAssertionTraitSetType(enum.Enum): - DISEASE = "Disease" - DRUG_RESPONSE = "DrugResponse" - FINDING = "Finding" - PHENOTYPE_INSTRUCITON = "PhenotypeInstruction" - TRAIT_CHOICE = "TraitChoice" - - -class ClinVarAssertionTraitSet(BaseModel): - model_config = ConfigDict(frozen=True) - - type: ClinVarAssertionTraitSetType - date_last_evaluated: typing.Optional[datetime.date] = None - traits: typing.List[ClinVarAssertionTrait] = [] - names: typing.List[AnnotatedTypedValue] = [] - symbols: typing.List[AnnotatedTypedValue] = [] - attributes: typing.List[ClinAsserTraitSetTypeAttribute] = [] - id: typing.Optional[int] = None - multiple_condition_explanation: typing.Optional[str] = None - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertionTraitSet": - return cls( - type=ClinVarAssertionTraitSetType(json_data["@Type"]), - date_last_evaluated=( - parse_datetime(json_data["@DateLastEvaluated"]).date() - if json_data.get("@DateLastEvaluated") - else None - ), - traits=[ - ClinVarAssertionTrait.from_json_data(raw_trait) - for raw_trait in force_list(json_data.get("Trait", [])) - ], - names=[ - AnnotatedTypedValue.from_json_data(raw_name) - for raw_name in force_list(json_data.get("Name", [])) - ], - symbols=[ - AnnotatedTypedValue.from_json_data(raw_symbol) - for raw_symbol in force_list(json_data.get("Symbol", [])) - ], - attributes=[ - ClinAsserTraitSetTypeAttribute.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - id=int(json_data["@ID"]) if json_data.get("@ID") else None, - multiple_condition_explanation=json_data.get("MultipleConditionExplanation"), - ) - - -class ClinVarAssertion(BaseModel): - """The ClinVarAssertion is the package of data as received from the submitter. During - integration with other submissions, the content may have been mapped to controlled values. - - Represents a ``ClinVarAssertion`` in the XML file. - """ - - model_config = ConfigDict(frozen=True) - - #: The submission's ID. - id: int - #: More detaield submission information. - submission_id: ClinVarSubmissionId - #: The ClinVar accession number. - clinvar_accession: ClinVarAssertionAccession - #: The assertion type. - assertion_type: AssertionTypeSCV - #: The record status - record_status: RecordStatus = RecordStatus.CURRENT - #: Optional element used only if there are multiple submitters. When there are multiple, - #: each is listed in this element. - additional_submitters: typing.List[Submitter] = [] - #: The list of SCV accessions this SCV record has replaced. - replaced_list: typing.List[RecordHistory] = [] - #: The clinical significance assertion. - clinical_significance: typing.List[ClinicalSignificanceTypeSCV] = [] - #: XrefType is used to identify data source(s) and their identifiers. Optional because - #: not all sources have an ID specific to the assertion. - external_ids: typing.List[Xref] = [] - #: Additional attribute sets. - attributes: typing.List[ClinVarAssertionAttributeSet] = [] - #: Observation information. - observed_in: typing.List[ObservationSet] = [] - #: Measurement information, mutually exlusive with ``genotype``. - measures: typing.Optional[MeasureSet] = None - #: Genotyping information, mutually exlusive with ``measure``. - genotypes: typing.Optional[GenotypeSet] = None - #: Traits associated with the disease. - traits: typing.Optional[ClinVarAssertionTraitSet] = None - #: Citations for the variant. - citations: typing.List[Citation] = [] - #: An optional study name. - study_name: typing.Optional[str] = None - #: An optional study description. - study_description: typing.Optional[str] = None - #: Optional comments. - comments: typing.List[Comment] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarAssertion": - return ClinVarAssertion( - id=int(json_data["@ID"]), - submission_id=ClinVarSubmissionId.from_json_data(json_data["ClinVarSubmissionID"]), - clinvar_accession=ClinVarAssertionAccession.from_json_data( - json_data["ClinVarAccession"] - ), - assertion_type=AssertionTypeSCV(json_data["Assertion"]["@Type"]), - additional_submitters=[ - Submitter.from_json_data(raw_submitter) - for raw_submitter in force_list( - json_data.get("AdditionalSubmitters", {}).get("SubmitterDescription", []) - ) - ], - replaced_list=[ - RecordHistory.from_json_data(raw_replaced) - for raw_replaced in force_list( - json_data.get("ReplacedList", {}).get("Replaced", []) - ) - ], - clinical_significance=[ - ClinicalSignificanceTypeSCV.from_json_data(raw_clinical_significance) - for raw_clinical_significance in force_list( - json_data.get("ClinicalSignificance", []) - ) - ], - external_ids=[ - Xref.from_json_data(raw_xref) - for raw_xref in force_list(json_data.get("ExternalID", [])) - ], - attributes=[ - ClinVarAssertionAttributeSet.from_json_data(raw_attribute) - for raw_attribute in force_list(json_data.get("AttributeSet", [])) - ], - observed_in=[ - ObservationSet.from_json_data(raw_observations) - for raw_observations in force_list(json_data.get("ObservedIn", [])) - ], - measures=( - MeasureSet.from_json_data(json_data["MeasureSet"]) - if json_data.get("MeasureSet") - else None - ), - genotypes=( - GenotypeSet.from_json_data(json_data["GenotypeSet"]) - if json_data.get("GenotypeSet") - else None - ), - traits=( - ClinVarAssertionTraitSet.from_json_data(json_data["TraitSet"]) - if "TraitSet" in json_data - else None - ), - citations=[ - Citation.from_json_data(raw_citation) - for raw_citation in force_list(json_data.get("Citation", [])) - ], - study_name=json_data.get("StudyName"), - study_description=json_data.get("StudyDescription"), - comments=[ - Comment.from_json_data(raw_comment) - for raw_comment in force_list(json_data.get("Comment", [])) - ], - ) - - -class ClinVarSet(BaseModel): - """A ```` in the ClinVar public XML file""" - - model_config = ConfigDict(frozen=True) - - #: The reference clinvar assertion as used in RCV records - reference_clinvar_assertion: ReferenceClinVarAssertion - #: The set's record status - record_status: RecordStatus = RecordStatus.CURRENT - #: The identifiers that this record replaces - replaces: typing.List[str] = [] - #: An optional title for the submission - title: typing.Optional[str] = None - #: The clinvar assertion - clinvar_assertions: typing.List[ClinVarAssertion] = [] - - @classmethod - def from_json_data(cls, json_data: dict) -> "ClinVarSet": - raw_clinvar_assertions = force_list(json_data["ClinVarAssertion"]) - - result = ClinVarSet( - record_status=RecordStatus(json_data["RecordStatus"]), - title=json_data.get("Title"), - replaces=force_list(json_data.get("Replaces", [])), - reference_clinvar_assertion=ReferenceClinVarAssertion.from_json_data( - json_data["ReferenceClinVarAssertion"] - ), - clinvar_assertions=[ - ClinVarAssertion.from_json_data(raw_cva) for raw_cva in raw_clinvar_assertions - ], - ) - return result diff --git a/clinvar_data/pbs/class_by_freq_pb2.py b/clinvar_data/pbs/class_by_freq_pb2.py index 216013b..5352a34 100644 --- a/clinvar_data/pbs/class_by_freq_pb2.py +++ b/clinvar_data/pbs/class_by_freq_pb2.py @@ -20,6 +20,7 @@ _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "clinvar_data.pbs.class_by_freq_pb2", _globals) if _descriptor._USE_C_DESCRIPTORS == False: + DESCRIPTOR._options = None _globals["_COARSECLINICALSIGNIFICANCE"]._serialized_start = 202 _globals["_COARSECLINICALSIGNIFICANCE"]._serialized_end = 406 diff --git a/clinvar_data/pbs/clinvar_public_pb2.py b/clinvar_data/pbs/clinvar_public_pb2.py index ce9a151..ffba121 100644 --- a/clinvar_data/pbs/clinvar_public_pb2.py +++ b/clinvar_data/pbs/clinvar_public_pb2.py @@ -15,56 +15,57 @@ from google.protobuf import timestamp_pb2 as 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_globals["_CLINVARVARIATIONRELEASE"]._serialized_end = 36052 # @@protoc_insertion_point(module_scope) diff --git a/clinvar_data/pbs/clinvar_public_pb2.pyi b/clinvar_data/pbs/clinvar_public_pb2.pyi index 3786435..5c17456 100644 --- a/clinvar_data/pbs/clinvar_public_pb2.pyi +++ b/clinvar_data/pbs/clinvar_public_pb2.pyi @@ -2296,8 +2296,6 @@ class Trait(google.protobuf.message.Message): """corresponds to "Finding member" """ NAMES_FIELD_NUMBER: builtins.int - SYMBOLS_FIELD_NUMBER: builtins.int - ATTRIBUTES_FIELD_NUMBER: builtins.int CITATIONS_FIELD_NUMBER: builtins.int XREFS_FIELD_NUMBER: builtins.int COMMENTS_FIELD_NUMBER: builtins.int @@ -2316,28 +2314,9 @@ class Trait(google.protobuf.message.Message): ]: """nested elements - names - - NB: in XSD this is explictely given as unbounded but XML always has - one element + Name(s) of the trait. """ - @property - def symbols( - self, - ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[ - global___GenericSetElement - ]: - """symbols (NB: never occur in the XML)""" - - @property - def attributes( - self, - ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[ - global___AttributeSetElement - ]: - """attributes (NB: never occur in the XML)""" - @property def citations( self, @@ -2366,8 +2345,6 @@ class Trait(google.protobuf.message.Message): self, *, names: collections.abc.Iterable[global___GenericSetElement] | None = ..., - symbols: collections.abc.Iterable[global___GenericSetElement] | None = ..., - attributes: collections.abc.Iterable[global___AttributeSetElement] | None = ..., citations: collections.abc.Iterable[global___Citation] | None = ..., xrefs: collections.abc.Iterable[global___Xref] | None = ..., comments: collections.abc.Iterable[global___Comment] | None = ..., @@ -2377,8 +2354,6 @@ class Trait(google.protobuf.message.Message): def ClearField( self, field_name: typing.Literal[ - "attributes", - b"attributes", "citations", b"citations", "comments", @@ -2387,8 +2362,6 @@ class Trait(google.protobuf.message.Message): b"names", "sources", b"sources", - "symbols", - b"symbols", "type", b"type", "xrefs", @@ -3422,18 +3395,14 @@ class AggregateClassificationSet(google.protobuf.message.Message): DESCRIPTOR: google.protobuf.descriptor.Descriptor GERMLINE_CLASSIFICATION_FIELD_NUMBER: builtins.int - SOMATIC_CLINICAL_IMPACTS_FIELD_NUMBER: builtins.int + SOMATIC_CLINICAL_IMPACT_FIELD_NUMBER: builtins.int ONCOGENICITY_CLASSIFICATION_FIELD_NUMBER: builtins.int @property def germline_classification(self) -> global___AggregatedGermlineClassification: """The aggregate germline classification.""" @property - def somatic_clinical_impacts( - self, - ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[ - global___AggregatedSomaticClinicalImpact - ]: + def somatic_clinical_impact(self) -> global___AggregatedSomaticClinicalImpact: """The aggregate somatic clinical impact.""" @property @@ -3444,9 +3413,7 @@ class AggregateClassificationSet(google.protobuf.message.Message): self, *, germline_classification: global___AggregatedGermlineClassification | None = ..., - somatic_clinical_impacts: ( - collections.abc.Iterable[global___AggregatedSomaticClinicalImpact] | None - ) = ..., + somatic_clinical_impact: global___AggregatedSomaticClinicalImpact | None = ..., oncogenicity_classification: global___AggregatedOncogenicityClassification | None = ..., ) -> None: ... def HasField( @@ -3456,10 +3423,14 @@ class AggregateClassificationSet(google.protobuf.message.Message): b"_germline_classification", "_oncogenicity_classification", b"_oncogenicity_classification", + "_somatic_clinical_impact", + b"_somatic_clinical_impact", "germline_classification", b"germline_classification", "oncogenicity_classification", b"oncogenicity_classification", + "somatic_clinical_impact", + b"somatic_clinical_impact", ], ) -> builtins.bool: ... def ClearField( @@ -3469,12 +3440,14 @@ class AggregateClassificationSet(google.protobuf.message.Message): b"_germline_classification", "_oncogenicity_classification", b"_oncogenicity_classification", + "_somatic_clinical_impact", + b"_somatic_clinical_impact", "germline_classification", b"germline_classification", "oncogenicity_classification", b"oncogenicity_classification", - "somatic_clinical_impacts", - b"somatic_clinical_impacts", + "somatic_clinical_impact", + b"somatic_clinical_impact", ], ) -> None: ... @typing.overload @@ -3488,6 +3461,10 @@ class AggregateClassificationSet(google.protobuf.message.Message): "_oncogenicity_classification", b"_oncogenicity_classification" ], ) -> typing.Literal["oncogenicity_classification"] | None: ... + @typing.overload + def WhichOneof( + self, oneof_group: typing.Literal["_somatic_clinical_impact", b"_somatic_clinical_impact"] + ) -> typing.Literal["somatic_clinical_impact"] | None: ... global___AggregateClassificationSet = AggregateClassificationSet @@ -3969,7 +3946,7 @@ class ClassificationScv(google.protobuf.message.Message): REVIEW_STATUS_FIELD_NUMBER: builtins.int GERMLINE_CLASSIFICATION_FIELD_NUMBER: builtins.int - SOMATIC_CLINICAL_IMPACTS_FIELD_NUMBER: builtins.int + SOMATIC_CLINICAL_IMPACT_FIELD_NUMBER: builtins.int ONCOGENICITY_CLASSIFICATION_FIELD_NUMBER: builtins.int EXPLANATION_OF_CLASSIFICATION_FIELD_NUMBER: builtins.int CLASSIFICATION_SCORES_FIELD_NUMBER: builtins.int @@ -3993,7 +3970,7 @@ class ClassificationScv(google.protobuf.message.Message): explanation_of_classification: builtins.str """Optional explanation of classification.""" @property - def somatic_clinical_impacts(self) -> global___ClassificationScv.SomaticClinicalImpact: + def somatic_clinical_impact(self) -> global___ClassificationScv.SomaticClinicalImpact: """Information on the clinical impact; mutually exlusive with `germline_classification` and `oncogenicity_classification`. """ @@ -4036,7 +4013,7 @@ class ClassificationScv(google.protobuf.message.Message): *, review_status: global___SubmitterReviewStatus.ValueType = ..., germline_classification: builtins.str | None = ..., - somatic_clinical_impacts: global___ClassificationScv.SomaticClinicalImpact | None = ..., + somatic_clinical_impact: global___ClassificationScv.SomaticClinicalImpact | None = ..., oncogenicity_classification: builtins.str | None = ..., explanation_of_classification: builtins.str | None = ..., classification_scores: ( @@ -4058,8 +4035,8 @@ class ClassificationScv(google.protobuf.message.Message): b"_germline_classification", "_oncogenicity_classification", b"_oncogenicity_classification", - "_somatic_clinical_impacts", - b"_somatic_clinical_impacts", + "_somatic_clinical_impact", + b"_somatic_clinical_impact", "date_last_evaluated", b"date_last_evaluated", "explanation_of_classification", @@ -4068,8 +4045,8 @@ class ClassificationScv(google.protobuf.message.Message): b"germline_classification", "oncogenicity_classification", b"oncogenicity_classification", - "somatic_clinical_impacts", - b"somatic_clinical_impacts", + "somatic_clinical_impact", + b"somatic_clinical_impact", ], ) -> builtins.bool: ... def ClearField( @@ -4083,8 +4060,8 @@ class ClassificationScv(google.protobuf.message.Message): b"_germline_classification", "_oncogenicity_classification", b"_oncogenicity_classification", - "_somatic_clinical_impacts", - b"_somatic_clinical_impacts", + "_somatic_clinical_impact", + b"_somatic_clinical_impact", "citations", b"citations", "classification_scores", @@ -4101,8 +4078,8 @@ class ClassificationScv(google.protobuf.message.Message): b"oncogenicity_classification", "review_status", b"review_status", - "somatic_clinical_impacts", - b"somatic_clinical_impacts", + "somatic_clinical_impact", + b"somatic_clinical_impact", "xrefs", b"xrefs", ], @@ -4131,8 +4108,8 @@ class ClassificationScv(google.protobuf.message.Message): ) -> typing.Literal["oncogenicity_classification"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing.Literal["_somatic_clinical_impacts", b"_somatic_clinical_impacts"] - ) -> typing.Literal["somatic_clinical_impacts"] | None: ... + self, oneof_group: typing.Literal["_somatic_clinical_impact", b"_somatic_clinical_impact"] + ) -> typing.Literal["somatic_clinical_impact"] | None: ... global___ClassificationScv = ClassificationScv @@ -6707,7 +6684,7 @@ class AlleleScv(google.protobuf.message.Message): ) -> typing.Literal["so_id"] | None: ... GENES_FIELD_NUMBER: builtins.int - NAMES_FIELD_NUMBER: builtins.int + NAME_FIELD_NUMBER: builtins.int VARIANT_TYPE_FIELD_NUMBER: builtins.int LOCATION_FIELD_NUMBER: builtins.int OTHER_NAMES_FIELD_NUMBER: builtins.int @@ -6739,9 +6716,7 @@ class AlleleScv(google.protobuf.message.Message): """ @property - def names( - self, - ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[global___OtherName]: + def name(self) -> global___OtherName: """Name provided by the submitter.""" @property @@ -6810,7 +6785,7 @@ class AlleleScv(google.protobuf.message.Message): self, *, genes: collections.abc.Iterable[global___AlleleScv.Gene] | None = ..., - names: collections.abc.Iterable[global___OtherName] | None = ..., + name: global___OtherName | None = ..., variant_type: builtins.str | None = ..., location: global___Location | None = ..., other_names: collections.abc.Iterable[global___OtherName] | None = ..., @@ -6840,6 +6815,8 @@ class AlleleScv(google.protobuf.message.Message): b"allele_id", "location", b"location", + "name", + b"name", "variant_type", b"variant_type", ], @@ -6869,8 +6846,8 @@ class AlleleScv(google.protobuf.message.Message): b"location", "molecular_consequences", b"molecular_consequences", - "names", - b"names", + "name", + b"name", "other_names", b"other_names", "protein_changes", @@ -6908,7 +6885,7 @@ class HaplotypeScv(google.protobuf.message.Message): SIMPLE_ALLELES_FIELD_NUMBER: builtins.int NAME_FIELD_NUMBER: builtins.int OTHER_NAMES_FIELD_NUMBER: builtins.int - CLASSIFICATION_FIELD_NUMBER: builtins.int + CLASSIFICATIONS_FIELD_NUMBER: builtins.int FUNCTIONAL_CONSEQUENCES_FIELD_NUMBER: builtins.int ATTRIBUTES_FIELD_NUMBER: builtins.int CITATIONS_FIELD_NUMBER: builtins.int @@ -6938,7 +6915,7 @@ class HaplotypeScv(google.protobuf.message.Message): """Names other than 'preferred' used for the haplotype.""" @property - def classification(self) -> global___AggregateClassificationSet: + def classifications(self) -> global___AggregateClassificationSet: """Classification of the variant.""" @property @@ -6981,7 +6958,7 @@ class HaplotypeScv(google.protobuf.message.Message): simple_alleles: collections.abc.Iterable[global___AlleleScv] | None = ..., name: builtins.str | None = ..., other_names: collections.abc.Iterable[global___OtherName] | None = ..., - classification: global___AggregateClassificationSet | None = ..., + classifications: global___AggregateClassificationSet | None = ..., functional_consequences: ( collections.abc.Iterable[global___FunctionalConsequence] | None ) = ..., @@ -6996,8 +6973,8 @@ class HaplotypeScv(google.protobuf.message.Message): def HasField( self, field_name: typing.Literal[ - "_classification", - b"_classification", + "_classifications", + b"_classifications", "_name", b"_name", "_number_of_chromosomes", @@ -7006,8 +6983,8 @@ class HaplotypeScv(google.protobuf.message.Message): b"_number_of_copies", "_variation_id", b"_variation_id", - "classification", - b"classification", + "classifications", + b"classifications", "name", b"name", "number_of_chromosomes", @@ -7021,8 +6998,8 @@ class HaplotypeScv(google.protobuf.message.Message): def ClearField( self, field_name: typing.Literal[ - "_classification", - b"_classification", + "_classifications", + b"_classifications", "_name", b"_name", "_number_of_chromosomes", @@ -7035,8 +7012,8 @@ class HaplotypeScv(google.protobuf.message.Message): b"attributes", "citations", b"citations", - "classification", - b"classification", + "classifications", + b"classifications", "comments", b"comments", "functional_consequences", @@ -7059,8 +7036,8 @@ class HaplotypeScv(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing.Literal["_classification", b"_classification"] - ) -> typing.Literal["classification"] | None: ... + self, oneof_group: typing.Literal["_classifications", b"_classifications"] + ) -> typing.Literal["classifications"] | None: ... @typing.overload def WhichOneof( self, oneof_group: typing.Literal["_name", b"_name"] @@ -8054,12 +8031,8 @@ class ClinicalAssertion(google.protobuf.message.Message): """Replaced list; mutually exclusive with replaces""" @property - def classifications( - self, - ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[ - global___ClassificationScv - ]: - """SCV classifications.""" + def classifications(self) -> global___ClassificationScv: + """SCV classification.""" @property def attributes( @@ -8133,7 +8106,7 @@ class ClinicalAssertion(google.protobuf.message.Message): record_status: global___ClinicalAssertion.RecordStatus.ValueType = ..., replaces: collections.abc.Iterable[builtins.str] | None = ..., replaceds: collections.abc.Iterable[global___ClinicalAssertionRecordHistory] | None = ..., - classifications: collections.abc.Iterable[global___ClassificationScv] | None = ..., + classifications: global___ClassificationScv | None = ..., assertion: global___Assertion.ValueType = ..., attributes: ( collections.abc.Iterable[global___ClinicalAssertion.AttributeSetElement] | None @@ -8171,6 +8144,8 @@ class ClinicalAssertion(google.protobuf.message.Message): b"_study_description", "_study_name", b"_study_name", + "classifications", + b"classifications", "clinvar_accession", b"clinvar_accession", "clinvar_submission_id", diff --git a/clinvar_data/pbs/extracted_vars_pb2.py b/clinvar_data/pbs/extracted_vars_pb2.py index 3a69f83..f2e1184 100644 --- a/clinvar_data/pbs/extracted_vars_pb2.py +++ b/clinvar_data/pbs/extracted_vars_pb2.py @@ -24,6 +24,7 @@ _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "clinvar_data.pbs.extracted_vars_pb2", _globals) if _descriptor._USE_C_DESCRIPTORS == False: + DESCRIPTOR._options = None _globals["_VARIATIONTYPE"]._serialized_start = 812 _globals["_VARIATIONTYPE"]._serialized_end = 1276 diff --git a/clinvar_data/pbs/gene_impact_pb2.py b/clinvar_data/pbs/gene_impact_pb2.py index 84033a9..2270e73 100644 --- a/clinvar_data/pbs/gene_impact_pb2.py +++ b/clinvar_data/pbs/gene_impact_pb2.py @@ -24,6 +24,7 @@ _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "clinvar_data.pbs.gene_impact_pb2", _globals) if _descriptor._USE_C_DESCRIPTORS == False: + DESCRIPTOR._options = None _globals["_GENEIMPACT"]._serialized_start = 458 _globals["_GENEIMPACT"]._serialized_end = 1091 diff --git a/clinvar_data/pbs/phenotype_link_pb2.py b/clinvar_data/pbs/phenotype_link_pb2.py index 71536fd..2420ef8 100644 --- a/clinvar_data/pbs/phenotype_link_pb2.py +++ b/clinvar_data/pbs/phenotype_link_pb2.py @@ -24,6 +24,7 @@ _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "clinvar_data.pbs.phenotype_link_pb2", _globals) if _descriptor._USE_C_DESCRIPTORS == False: + DESCRIPTOR._options = None _globals["_GENEPHENOTYPERECORD"]._serialized_start = 114 _globals["_GENEPHENOTYPERECORD"]._serialized_end = 402 diff --git a/clinvar_data/phenotype_link.py b/clinvar_data/phenotype_link.py index db3918b..d65dcea 100644 --- a/clinvar_data/phenotype_link.py +++ b/clinvar_data/phenotype_link.py @@ -60,14 +60,14 @@ def run_report(path_input: str, path_output: str, needs_hpo_terms: bool = True): version=clinical_assertion.clinvar_accession.version, ) germline_classification: str | None = None - for classification in clinical_assertion.classifications: - if ( - classification.HasField("germline_classification") - # and "pathogenic" in classification.germline_classification.lower() - ): - germline_classification = classification.germline_classification - print("\n\n", germline_classification) - break + if ( + clinical_assertion.HasField("classifications") + and clinical_assertion.classifications.HasField("germline_classification") + # and "pathogenic" in classification.germline_classification.lower() + ): + germline_classification = ( + clinical_assertion.classifications.germline_classification + ) if not germline_classification: continue diff --git a/protos/clinvar_data/pbs/clinvar_public.proto b/protos/clinvar_data/pbs/clinvar_public.proto index d471690..9e48bd2 100644 --- a/protos/clinvar_data/pbs/clinvar_public.proto +++ b/protos/clinvar_data/pbs/clinvar_public.proto @@ -731,28 +731,21 @@ message Trait { /* nested elements */ - // names - // - // NB: in XSD this is explictely given as unbounded but XML always has - // one element + // Name(s) of the trait. repeated GenericSetElement names = 1; - // symbols (NB: never occur in the XML) - repeated GenericSetElement symbols = 2; - // attributes (NB: never occur in the XML) - repeated AttributeSetElement attributes = 3; // Citation list. - repeated Citation citations = 4; + repeated Citation citations = 2; // Xref list. - repeated Xref xrefs = 5; + repeated Xref xrefs = 3; // Comment list. - repeated Comment comments = 6; + repeated Comment comments = 4; // Sources - repeated string sources = 7; + repeated string sources = 5; /* attributes */ // Trait type. - Type type = 8; + Type type = 6; } // names @@ -985,7 +978,7 @@ message AggregateClassificationSet { // The aggregate germline classification. optional AggregatedGermlineClassification germline_classification = 1; // The aggregate somatic clinical impact. - repeated AggregatedSomaticClinicalImpact somatic_clinical_impacts = 2; + optional AggregatedSomaticClinicalImpact somatic_clinical_impact = 2; // The aggregate oncogenicity classification. optional AggregatedOncogenicityClassification oncogenicity_classification = 3; } @@ -1116,7 +1109,7 @@ message ClassificationScv { optional string germline_classification = 2; // Information on the clinical impact; mutually exlusive with `germline_classification` // and `oncogenicity_classification`. - optional SomaticClinicalImpact somatic_clinical_impacts = 3; + optional SomaticClinicalImpact somatic_clinical_impact = 3; // The oncogenicity classification; mutually exlusive with `germline_classification` // and `oncogenicity_classification`. optional string oncogenicity_classification = 4; @@ -1770,7 +1763,7 @@ message AlleleScv { // being reported. repeated Gene genes = 1; // Name provided by the submitter. - repeated OtherName names = 2; + OtherName name = 2; // Variant type. optional string variant_type = 3; // Location. @@ -1811,7 +1804,7 @@ message HaplotypeScv { // Names other than 'preferred' used for the haplotype. repeated OtherName other_names = 3; // Classification of the variant. - optional AggregateClassificationSet classification = 4; + optional AggregateClassificationSet classifications = 4; // Functional consequences of the variant. repeated FunctionalConsequence functional_consequences = 5; // List of attributes. @@ -2129,8 +2122,8 @@ message ClinicalAssertion { // Replaced list; mutually exclusive with replaces repeated ClinicalAssertionRecordHistory replaceds = 6; - // SCV classifications. - repeated ClassificationScv classifications = 7; + // SCV classification. + ClassificationScv classifications = 7; // The assertion. Assertion assertion = 8; // Attributes. diff --git a/tests/clinvar_data/data/_extract_variation_archives.py b/tests/clinvar_data/data/_extract_variation_archives.py index 1e2f337..2922ee2 100755 --- a/tests/clinvar_data/data/_extract_variation_archives.py +++ b/tests/clinvar_data/data/_extract_variation_archives.py @@ -163,7 +163,7 @@ class Target: def main() -> int: args = sys.argv if len(args) != 2: - print("Usage: extract_variation_archives.py ") + print("Usage: _extract_variation_archives.py ") return 1 input_xml = args[1] diff --git a/tests/clinvar_data/data/ex_kynu.jsonl b/tests/clinvar_data/data/ex_kynu.jsonl index 32455fe..e27aa9b 100644 --- a/tests/clinvar_data/data/ex_kynu.jsonl +++ b/tests/clinvar_data/data/ex_kynu.jsonl @@ -1 +1 @@ -{"variationId": "978270", "variationName": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "single nucleotide variant", "dateCreated": "2020-09-27T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "accession": "VCV000978270", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["2q22.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142877664, "stop": 143055833, "displayStart": 142877664, "displayStop": 143055833, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143635194, "stop": 143799884, "displayStart": 143635194, "displayStop": 143799884, "strand": "+"}]}], "omims": ["605197"], "fullName": "kynureninase", "geneId": "8942", "hgncId": "HGNC:6469", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "canonicalSpdi": "NC_000002.12:142927693:G:C", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["2q22.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142927694, "stop": 142927694, "displayStart": 142927694, "displayStop": 142927694, "variantLength": 1, "positionVcf": 142927694, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143685263, "stop": 143685263, "displayStart": 143685263, "displayStop": 143685263, "variantLength": 1, "referenceAllele": "G", "alternateAllele": "C", "positionVcf": 143685263, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}]}], "proteinChanges": ["W109S"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NC_000002.11:g.143685263G>C", "sequenceAccessionVersion": "NC_000002.11", "sequenceAccession": "NC_000002", "sequenceVersion": 11, "change": "g.143685263G>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000002.12:g.142927694G>C", "sequenceAccessionVersion": "NC_000002.12", "sequenceAccession": "NC_000002", "sequenceVersion": 12, "change": "g.142927694G>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_023254.1:g.55069G>C", "sequenceAccessionVersion": "NG_023254.1", "sequenceAccession": "NG_023254", "sequenceVersion": 1, "change": "g.55069G>C"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001032998.2:c.326G>C", "sequenceAccessionVersion": "NM_001032998.2", "sequenceAccession": "NM_001032998", "sequenceVersion": 2, "change": "c.326G>C"}, "proteinExpression": {"expression": "NP_001028170.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_001028170.1", "sequenceAccession": "NP_001028170", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_001199241.2:c.326G>C", "sequenceAccessionVersion": "NM_001199241.2", "sequenceAccession": "NM_001199241", "sequenceVersion": 2, "change": "c.326G>C"}, "proteinExpression": {"expression": "NP_001186170.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_001186170.1", "sequenceAccession": "NP_001186170", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_003937.3:c.326G>C", "sequenceAccessionVersion": "NM_003937.3", "sequenceAccession": "NM_003937", "sequenceVersion": 3, "change": "c.326G>C", "maneSelect": true}, "proteinExpression": {"expression": "NP_003928.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_003928.1", "sequenceAccession": "NP_003928", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "dbSNP", "id": "780720490", "type": "rs"}], "alleleId": "966396", "variationId": "978270"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Catel-Manzke syndrome", "db": "MedGen", "id": "C1844887"}], "traitSetId": "20503"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "accession": "RCV001256675", "version": 1}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "conditions": [{"traits": [{"names": [{"value": "Hyperphalangy-clinodactyly of index finger with Pierre Robin syndrome", "type": "Alternate"}, {"value": "Pierre Robin syndrome with hyperphalangy and clinodactyly", "type": "Alternate"}, {"value": "Palatodigital syndrome Catel-Manzke type", "type": "Alternate"}, {"value": "Index finger anomaly with Pierre Robin syndrome", "type": "Alternate"}, {"value": "Catel-Manzke syndrome", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0014507"}]}, {"value": "MICROGNATHIA DIGITAL SYNDROME", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "symbols": [{"value": "CATMANS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "28"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "28"}]}], "xrefs": [{"db": "Orphanet", "id": "1388"}, {"db": "MedGen", "id": "C1844887"}, {"db": "MONDO", "id": "MONDO:0014507"}, {"db": "OMIM", "id": "616145", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "20503", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "20200511-001-003", "localKeyIsSubmitted": false, "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001433049", "version": 1, "submitterIdentifiers": {"submitterName": "Institute for Medical Genetics and Human Genetics, Charit\u00e9 - Universit\u00e4tsmedizin Berlin", "orgId": "505735", "orgCategory": "clinic", "orgAbbreviation": "Charit\u00e9 - Universit\u00e4tsmedizin"}, "dateUpdated": "2020-09-27T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "CUBI - Core Unit Bioinformatics, Berlin Institute of Health", "orgId": "507461", "orgCategory": "laboratory"}, "type": "TYPE_SECONDARY"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}, {"attribute": {"value": "Antenatal"}, "type": "TYPE_AGE_OF_ONSET"}, {"attribute": {"value": "Autosomal recessive inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "tissue": "blood", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_MALE", "familyData": {"pedigreeId": "PM31923704-3"}, "citations": [{"ids": [{"value": "31923704", "source": "PubMed"}]}]}, "observedData": [{"attributes": [{"base": {"integerValue": "2"}, "type": "TYPE_COMPOUND_HETEROZYGOUS"}]}, {"attributes": [{"base": {"value": "PM31923704-3"}, "type": "TYPE_SAMPLE_LOCAL_ID"}]}], "traitSet": {"traits": [{"names": [{"value": "Finger hyperphalangy", "type": "Preferred"}], "xrefs": [{"db": "HP", "id": "HP:0030367"}]}], "type": "TYPE_FINDING"}}], "simpleAllele": {"genes": [{"symbol": "KYNU"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 143685263, "stop": 143685263, "referenceAllele": "G", "alternateAllele": "C"}]}}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "id": "2829930"}], "traitMappings": [{"medgens": [{"name": "Finger hyperphalangy", "cui": "C4072906"}], "clinicalAssertionId": "2829930", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Finger hyperphalangy", "mappingRef": "Preferred"}, {"medgens": [{"name": "Catel-Manzke syndrome", "cui": "C1844887"}], "clinicalAssertionId": "2829930", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "616145", "mappingRef": "OMIM"}]}} +{"variationId": "978270", "variationName": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "single nucleotide variant", "dateCreated": "2020-09-27T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "accession": "VCV000978270", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["2q22.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142877664, "stop": 143055833, "displayStart": 142877664, "displayStop": 143055833, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143635194, "stop": 143799884, "displayStart": 143635194, "displayStop": 143799884, "strand": "+"}]}], "omims": ["605197"], "fullName": "kynureninase", "geneId": "8942", "hgncId": "HGNC:6469", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "canonicalSpdi": "NC_000002.12:142927693:G:C", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["2q22.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142927694, "stop": 142927694, "displayStart": 142927694, "displayStop": 142927694, "variantLength": 1, "positionVcf": 142927694, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143685263, "stop": 143685263, "displayStart": 143685263, "displayStop": 143685263, "variantLength": 1, "referenceAllele": "G", "alternateAllele": "C", "positionVcf": 143685263, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}]}], "proteinChanges": ["W109S"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NC_000002.11:g.143685263G>C", "sequenceAccessionVersion": "NC_000002.11", "sequenceAccession": "NC_000002", "sequenceVersion": 11, "change": "g.143685263G>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000002.12:g.142927694G>C", "sequenceAccessionVersion": "NC_000002.12", "sequenceAccession": "NC_000002", "sequenceVersion": 12, "change": "g.142927694G>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_023254.1:g.55069G>C", "sequenceAccessionVersion": "NG_023254.1", "sequenceAccession": "NG_023254", "sequenceVersion": 1, "change": "g.55069G>C"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001032998.2:c.326G>C", "sequenceAccessionVersion": "NM_001032998.2", "sequenceAccession": "NM_001032998", "sequenceVersion": 2, "change": "c.326G>C"}, "proteinExpression": {"expression": "NP_001028170.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_001028170.1", "sequenceAccession": "NP_001028170", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_001199241.2:c.326G>C", "sequenceAccessionVersion": "NM_001199241.2", "sequenceAccession": "NM_001199241", "sequenceVersion": 2, "change": "c.326G>C"}, "proteinExpression": {"expression": "NP_001186170.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_001186170.1", "sequenceAccession": "NP_001186170", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_003937.3:c.326G>C", "sequenceAccessionVersion": "NM_003937.3", "sequenceAccession": "NM_003937", "sequenceVersion": 3, "change": "c.326G>C", "maneSelect": true}, "proteinExpression": {"expression": "NP_003928.1:p.Trp109Ser", "sequenceAccessionVersion": "NP_003928.1", "sequenceAccession": "NP_003928", "sequenceVersion": 1, "change": "p.Trp109Ser"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "dbSNP", "id": "780720490", "type": "rs"}], "alleleId": "966396", "variationId": "978270"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Catel-Manzke syndrome", "db": "MedGen", "id": "C1844887"}], "traitSetId": "20503"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "accession": "RCV001256675", "version": 1}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "conditions": [{"traits": [{"names": [{"value": "Hyperphalangy-clinodactyly of index finger with Pierre Robin syndrome", "type": "Alternate"}, {"value": "Pierre Robin syndrome with hyperphalangy and clinodactyly", "type": "Alternate"}, {"value": "Palatodigital syndrome Catel-Manzke type", "type": "Alternate"}, {"value": "Index finger anomaly with Pierre Robin syndrome", "type": "Alternate"}, {"value": "Catel-Manzke syndrome", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0014507"}]}, {"value": "MICROGNATHIA DIGITAL SYNDROME", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "symbols": [{"value": "CATMANS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "28"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "28"}]}], "xrefs": [{"db": "Orphanet", "id": "1388"}, {"db": "MedGen", "id": "C1844887"}, {"db": "MONDO", "id": "MONDO:0014507"}, {"db": "OMIM", "id": "616145", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "20503", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "20200511-001-003", "localKeyIsSubmitted": false, "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001433049", "version": 1, "submitterIdentifiers": {"submitterName": "Institute for Medical Genetics and Human Genetics, Charit\u00e9 - Universit\u00e4tsmedizin Berlin", "orgId": "505735", "orgCategory": "clinic", "orgAbbreviation": "Charit\u00e9 - Universit\u00e4tsmedizin"}, "dateUpdated": "2020-09-27T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "CUBI - Core Unit Bioinformatics, Berlin Institute of Health", "orgId": "507461", "orgCategory": "laboratory"}, "type": "TYPE_SECONDARY"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}, {"attribute": {"value": "Antenatal"}, "type": "TYPE_AGE_OF_ONSET"}, {"attribute": {"value": "Autosomal recessive inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "tissue": "blood", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_MALE", "familyData": {"pedigreeId": "PM31923704-3"}, "citations": [{"ids": [{"value": "31923704", "source": "PubMed"}]}]}, "observedData": [{"attributes": [{"base": {"integerValue": "2"}, "type": "TYPE_COMPOUND_HETEROZYGOUS"}]}, {"attributes": [{"base": {"value": "PM31923704-3"}, "type": "TYPE_SAMPLE_LOCAL_ID"}]}], "traitSet": {"traits": [{"names": [{"value": "Finger hyperphalangy", "type": "Preferred"}], "xrefs": [{"db": "HP", "id": "HP:0030367"}]}], "type": "TYPE_FINDING"}}], "simpleAllele": {"genes": [{"symbol": "KYNU"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 143685263, "stop": 143685263, "referenceAllele": "G", "alternateAllele": "C"}]}}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "616145", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "id": "2829930"}], "traitMappings": [{"medgens": [{"name": "Finger hyperphalangy", "cui": "C4072906"}], "clinicalAssertionId": "2829930", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Finger hyperphalangy", "mappingRef": "Preferred"}, {"medgens": [{"name": "Catel-Manzke syndrome", "cui": "C1844887"}], "clinicalAssertionId": "2829930", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "616145", "mappingRef": "OMIM"}]}} diff --git a/tests/clinvar_data/data/one_record.xml.gz b/tests/clinvar_data/data/one_record.xml.gz index 0ff1ede..6e416ed 100644 Binary files a/tests/clinvar_data/data/one_record.xml.gz and b/tests/clinvar_data/data/one_record.xml.gz differ diff --git a/tests/clinvar_data/data/record_with_submitter.jsonl b/tests/clinvar_data/data/record_with_submitter.jsonl index 5bf0184..45db286 100644 --- a/tests/clinvar_data/data/record_with_submitter.jsonl +++ b/tests/clinvar_data/data/record_with_submitter.jsonl @@ -1 +1 @@ -{"variationId": "253751", "variationName": "GRCh37/hg19 2p11.2(chr2:86269067-86509326)x3", "variationType": "copy number gain", "dateCreated": "2016-09-04T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2016-09-04T00:00:00Z", "accession": "VCV000253751", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["2p11.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 86213993, "stop": 86338083, "displayStart": 86213993, "displayStop": 86338083, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 86441115, "stop": 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"c.529G>C", "maneSelect": true}, "proteinExpression": {"expression": "NP_037451.1:p.Gly177Arg", "sequenceAccessionVersion": "NP_037451.1", "sequenceAccession": "NP_037451", "sequenceVersion": 1, "change": "p.Gly177Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA114576"}, {"db": "OMIM", "id": "611632.0002", "type": "Allelic variant"}, {"db": "dbSNP", "id": "118203946", "type": "rs"}], "alleleId": "15896", "variationId": "857"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Schnyder crystalline corneal dystrophy", "db": "MedGen", "id": "C0271287"}], "traitSetId": "225"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2013-02-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_013319.3(UBIAD1):c.529G>C (p.Gly177Arg) AND Schnyder crystalline corneal dystrophy", "accession": "RCV000000905", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "17962451", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "18176953", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "23169578", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Corneal dystrophy crystalline of Schnyder", "type": "Alternate"}, {"value": "Schnyder crystalline corneal dystrophy", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "Corneal+Dystrophy+Crystalline+of+Schnyder/1907"}, {"db": "SNOMED CT", "id": "419395007"}]}, {"value": "Schnyder corneal dystrophy", "type": "Alternate", "xrefs": [{"db": "MONDO", "id": "MONDO:0007374"}]}, {"value": "Crystalline corneal 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"proteinExpression": {"expression": "NP_079160.1:p.His98Arg", "sequenceAccessionVersion": "NP_079160.1", "sequenceAccession": "NP_079160", "sequenceVersion": 1, "change": "p.His98Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA115109"}, {"db": "UniProtKB", "id": "Q9H9P8#VAR_025685"}, {"db": "OMIM", "id": "609584.0006", "type": "Allelic variant"}, {"db": "dbSNP", "id": "267607206", "type": "rs"}], "alleleId": "16651", "variationId": "1612"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "L-2-hydroxyglutaric aciduria", "db": "MedGen", "id": "C1855995"}], "traitSetId": "414"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2010-01-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.293A>G (p.His98Arg) AND L-2-hydroxyglutaric aciduria", "accession": "RCV000001679", "version": 4}, {"classifiedConditionList": {"classifiedConditions": [{"value": "not provided", "db": "MedGen", "id": "CN517202"}], "traitSetId": "9460"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2017-10-05T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.293A>G (p.His98Arg) AND not provided", "accession": "RCV000522298", "version": 1}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "19911013", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "not provided", "type": "Preferred", "xrefs": [{"db": "Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre", "id": "13DG0619"}]}, {"value": "none provided", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"value": "The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."}, "type": "public definition"}}], "xrefs": [{"db": "MedGen", "id": "CN517202"}]}], "type": "TYPE_DISEASE", "id": "9460", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "L-2-hydroxyglutaric aciduria", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "L-2-hydroxyglutaric+aciduria/4061"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144"}, {"db": "MONDO", "id": "MONDO:0009370"}]}], "symbols": [{"value": "L2HGA", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "10472"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10472"}]}], "xrefs": [{"db": "Orphanet", "id": "79314"}, {"db": "MedGen", "id": "C1855995"}, {"db": "MONDO", "id": "MONDO:0009370"}, {"db": "OMIM", "id": "236792", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "414"}], "dateLastEvaluated": "2017-10-05T00:00:00Z", "dateCreated": "2017-11-10T00:00:00Z", "mostRecentSubmission": "2017-12-19T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "609584.0006_L-2-HYDROXYGLUTARIC ACIDURIA", "title": "L2HGDH, HIS98ARG_L-2-HYDROXYGLUTARIC ACIDURIA"}, "clinvarAccession": {"accession": "SCV000021835", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-11-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-01-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 unrelated Portuguese patients with L-2-hydroxyglutaric aciduria (L2HGA; 236792), Vilarinho et al. (2010) identified a homozygous 293A-G transition in the L2HGDH gene, resulting in a his98-to-arg (H98R) substitution in a conserved residue."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "19911013", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "names": [{"value": "L2HGDH, HIS98ARG"}], "variantType": "Variation", "otherNames": [{"value": "HIS98ARG", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "609584.0006", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "L-2-HYDROXYGLUTARIC ACIDURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21835"}, {"clinvarSubmissionId": {"localKey": "GDX:742576|Not Provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV000617755", "version": 2, "submitterIdentifiers": {"submitterName": "GeneDx", "orgId": "26957", "orgCategory": "laboratory"}, "dateUpdated": "2017-12-19T00:00:00Z", "dateCreated": "2017-12-19T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "The H98R variant in the L2HGDH gene has been reported previously in the heterozygous state, in the presence of a second L2HGDH variant, and in the homozygous state, in multiple unrelated individuals with L-2-hydroxyglutaric aciduria, intellectual disability, and leukodystrophy (Vilarinho et al., 2005; Vilarinho et al., 2010). A different missense variant at the same residue, H98Y, has also been reported in the homozygous state in individuals with L-2-hydroxyglutaric aciduria (Top\u00c3\u00a7u et al., 2004; Haliloglu et al., 2008). The H98R variant is not observed in large population cohorts (Lek et al., 2016). The H98R variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret H98R as a likely pathogenic variant."}], "dateLastEvaluated": "2017-10-05T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "GeneDx Variant Classification (06012015)"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/dhtz9flo/genedx_interprules_final_061215.pdf"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_14", "start": 50768850, "stop": 50768850, "variantLength": 1, "referenceAllele": "T", "alternateAllele": "C"}]}, "attributes": [{"attribute": {"base": {"value": "NM_024884.2:c.293A>G"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "Not Provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB5098196"], "id": "1204167"}], "traitMappings": [{"medgens": [{"name": "L-2-hydroxyglutaric aciduria", "cui": "C1855995"}], "clinicalAssertionId": "21835", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "L-2-HYDROXYGLUTARIC ACIDURIA", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "CN517202"}], "clinicalAssertionId": "1204167", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Not Provided", "mappingRef": "Preferred"}]}} -{"variationId": "1190", "variationName": "NM_001029871.4(RSPO4):c.194A>G (p.Gln65Arg)", "variationType": "single nucleotide variant", "dateCreated": "2019-09-23T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2019-09-23T00:00:00Z", "accession": "VCV000001190", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["20p13"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 958452, "stop": 1002311, "displayStart": 958452, "displayStop": 1002311, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_20", "accession": "NC_000020.10", "start": 939094, "stop": 982906, "displayStart": 939094, "displayStop": 982906, "strand": "-"}]}], "omims": ["610573"], "fullName": "R-spondin 4", "geneId": "343637", "hgncId": "HGNC:16175", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_001029871.4(RSPO4):c.194A>G (p.Gln65Arg)", "canonicalSpdi": "NC_000020.11:968023:T:C", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["20p13"], "sequenceLocations": 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"assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_013043.1:g.39241A>G", "sequenceAccessionVersion": "NG_013043.1", "sequenceAccession": "NG_013043", "sequenceVersion": 1, "change": "g.39241A>G"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001029871.4:c.194A>G", "sequenceAccessionVersion": "NM_001029871.4", "sequenceAccession": "NM_001029871", "sequenceVersion": 4, "change": "c.194A>G", "maneSelect": true}, "proteinExpression": {"expression": "NP_001025042.2:p.Gln65Arg", "sequenceAccessionVersion": "NP_001025042.2", "sequenceAccession": "NP_001025042", "sequenceVersion": 2, "change": "p.Gln65Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_001040007.3:c.194A>G", "sequenceAccessionVersion": "NM_001040007.3", "sequenceAccession": "NM_001040007", "sequenceVersion": 3, "change": "c.194A>G"}, "proteinExpression": {"expression": "NP_001035096.1:p.Gln65Arg", "sequenceAccessionVersion": "NP_001035096.1", "sequenceAccession": "NP_001035096", "sequenceVersion": 1, "change": "p.Gln65Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NC_000020.10:g.948667T>C", "sequenceAccessionVersion": "NC_000020.10", "sequenceAccession": "NC_000020", "sequenceVersion": 10, "change": "g.948667T>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}], "xrefs": [{"db": "ClinGen", "id": "CA114825"}, {"db": "UniProtKB", "id": "Q2I0M5#VAR_030399"}, {"db": "OMIM", "id": "610573.0001", "type": "Allelic variant"}, {"db": "dbSNP", "id": "74315420", "type": "rs"}], "alleleId": "16229", "variationId": "1190"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Anonychia", "db": "MedGen", "id": "C0265998"}], "traitSetId": "316"}, "rcvClassifications": 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CONGENITAL, 4", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "206800", "type": "MIM"}, {"db": "OMIM", "id": "610573.0007", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0003", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0001", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0002", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0004", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0005", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0006", "type": "Allelic variant"}, {"db": "OMIM", "id": "610573.0008", "type": "Allelic variant"}]}, {"value": "ANONYCHIA/HYPONYCHIA CONGENITA", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "206800", "type": "MIM"}]}, {"value": "ANONYCHIA TOTALIS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "206800", "type": "MIM"}]}], "symbols": [{"value": "NDNC4", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "206800", "type": "MIM"}]}], "xrefs": [{"db": "Orphanet", "id": "79143"}, 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(2006) demonstrated homozygosity for a missense mutation, gln65 to arg (Q65R), in the RSPO4 gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "4702713", "source": "PubMed"}]}, {"ids": [{"value": "17041604", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "206800", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "RSPO4"}], "names": [{"value": "RSPO4, GLN65ARG"}], "variantType": "Variation", "otherNames": [{"value": "GLN65ARG", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "610573.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21399"}], "traitMappings": [{"medgens": [{"name": "Anonychia", "cui": "C0265998"}], "clinicalAssertionId": "21399", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4", "mappingRef": "Preferred"}]}} -{"variationId": "2497", "variationName": "NM_000127.3(EXT1):c.528_535del (p.Lys177fs)", "variationType": "Deletion", "dateCreated": "2020-07-27T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2020-07-27T00:00:00Z", "accession": "VCV000002497", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["8q24.11"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_8", "accession": "NC_000008.11", "start": 117794490, "stop": 118111826, "displayStart": 117794490, "displayStop": 118111826, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_8", "accession": "NC_000008.10", "start": 118811601, "stop": 119124057, "displayStart": 118811601, "displayStop": 119124057, "strand": "-"}]}], "omims": ["608177"], "haploinsufficiency": {"value": "Sufficient 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"geneId": "23092", "hgncId": "HGNC:17073", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED"}], "name": "ARHGAP26, 52-BP INS", "variantTypes": ["Insertion"], "locations": [{"cytogeneticLocations": ["5q31"]}], "otherNames": [{"value": "52-BP INS"}], "xrefs": [{"db": "OMIM", "id": "605370.0002", "type": "Allelic variant"}], "alleleId": "20092", "variationId": "5053"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Juvenile myelomonocytic leukemia", "db": "MedGen", "id": "C0349639"}], "traitSetId": "99"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2000-08-01T00:00:00Z", "submissionCount": 1}}}, "title": "ARHGAP26, 52-BP INS AND Juvenile myelomonocytic leukemia", "accession": "RCV000005356", "version": 4}]}, "classifications": 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"general"}], "conditions": [{"traits": [{"names": [{"value": "Classic Hodgkin lymphoma", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0009348"}]}, {"value": "Hodgkin lymphoma", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Hodgkin+lymphoma/3444"}, {"db": "Human Phenotype Ontology", "id": "HP:0012189"}]}], "symbols": [{"value": "CHL", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "236000", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "16529"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "16529"}]}], "citations": [{"url": "https://www.nccn.org/professionals/physician_gls/pdf/hodgkins.pdf", "citationText": "NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines\u00ae) Hodgkin Lymphoma, 2022", "type": "practice guideline", "abbrev": "NCCN, 2022"}], "xrefs": [{"db": "Orphanet", "id": "391"}, {"db": "MedGen", "id": "C0019829"}, {"db": "MONDO", "id": "MONDO:0009348"}, {"db": "OMIM", "id": 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(2009) analyzed the KLHDC8B gene in 52 probands from families with 2 or more individuals with classic Hodgkin lymphoma (236000) and identified a +28C-T transition at a highly conserved nucleotide in the 5-prime UTR that was present in probands from 3 (5.8%) of 52 families compared with 4 (1.3%) of 307 controls (odds ratio, 4.64; 95% confidence interval, 1.01-21.4). The variant segregated with disease, and individuals heterozygous for the T allele were found to produce lower levels of KLHDC8B than those homozygous for the more common C allele. Studies in transfected HeLA cells demonstrated an approximately 50% reduction in translation of mRNA with the T allele compared to the C allele."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "19706467", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "236000", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "KLHDC8B"}], "names": [{"value": "KLHDC8B, 5-PRIME UTR, +28C-T"}], "variantType": "Variation", "otherNames": [{"value": "5-PRIME UTR, +28C-T", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613169.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "HODGKIN LYMPHOMA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20441"}], "traitMappings": [{"medgens": [{"name": "Classic Hodgkin lymphoma", "cui": "C0019829"}], "clinicalAssertionId": "20441", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "HODGKIN LYMPHOMA", "mappingRef": "Preferred"}]}} -{"variationId": "407", "variationName": "NM_144639.3(UROC1):c.1348C>T (p.Arg450Cys)", "variationType": "single nucleotide variant", "dateCreated": "2015-05-18T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": "2015-05-18T00:00:00Z", "accession": "VCV000000407", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["3q21.3"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_3", "accession": "NC_000003.12", "start": 126481166, "stop": 126517773, "displayStart": 126481166, "displayStop": 126517773, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_3", "accession": "NC_000003.11", "start": 126200007, "stop": 126236615, "displayStart": 126200007, "displayStop": 126236615, "strand": "-"}]}], "omims": ["613012"], "fullName": "urocanate hydratase 1", "geneId": "131669", "hgncId": "HGNC:26444", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_144639.3(UROC1):c.1348C>T (p.Arg450Cys)", "canonicalSpdi": "NC_000003.12:126498140:G:A", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["3q21.3"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_3", "accession": "NC_000003.12", "start": 126498141, "stop": 126498141, "displayStart": 126498141, "displayStop": 126498141, "variantLength": 1, "positionVcf": 126498141, "referenceAlleleVcf": "G", "alternateAlleleVcf": "A"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_3", "accession": "NC_000003.11", "start": 126216984, "stop": 126216984, "displayStart": 126216984, "displayStop": 126216984, "variantLength": 1, "positionVcf": 126216984, "referenceAlleleVcf": "G", "alternateAlleleVcf": "A"}]}], "proteinChanges": ["R450C", "R510C"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NM_001165974.2:c.1528C>T", "sequenceAccessionVersion": "NM_001165974.2", "sequenceAccession": "NM_001165974", "sequenceVersion": 2, "change": "c.1528C>T"}, "proteinExpression": {"expression": "NP_001159446.1:p.Arg510Cys", "sequenceAccessionVersion": "NP_001159446.1", "sequenceAccession": "NP_001159446", "sequenceVersion": 1, "change": "p.Arg510Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_144639.3:c.1348C>T", "sequenceAccessionVersion": "NM_144639.3", "sequenceAccession": "NM_144639", "sequenceVersion": 3, "change": "c.1348C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_653240.1:p.Arg450Cys", "sequenceAccessionVersion": "NP_653240.1", "sequenceAccession": "NP_653240", "sequenceVersion": 1, "change": "p.Arg450Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, 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"minorAllele": "A"}, "alleleId": "15446", "variationId": "407"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Urocanate hydratase deficiency", "db": "MedGen", "id": "C0268514"}], "traitSetId": "111"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2009-06-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_144639.3(UROC1):c.1348C>T (p.Arg450Cys) AND Urocanate hydratase deficiency", "accession": "RCV000000434", "version": 3}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "19304569", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Urocanate hydratase deficiency", "type": "Preferred", "xrefs": [{"db": 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"mostRecentSubmission": "2015-05-18T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613012.0001_UROCANASE DEFICIENCY (1 family)", "title": "UROC1, ARG450CYS_UROCANASE DEFICIENCY (1 family)"}, "clinvarAccession": {"accession": "SCV000020582", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-05-18T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2009-06-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED", "familyData": {"numFamilies": 1}}, "observedData": [{"attributes": [{"base": {"value": "In a 19-year-old Spanish woman with urocanic aciduria, mental retardation, and ataxia (UROCD; 276880), Espinos et al. (2009) identified compound heterozygosity for a 1348C-T transition in exon 14 of the UROC1 gene, resulting in an arg450-to-cys (R450C) substitution at a highly conserved residue, and a 209T-C transition in exon 2 (613012.0002), resulting in a leu70to-pro (L70P) substitution in the N-terminal alpha helix. Both mutations were predicted to have a pathologic effect, and enzyme activity was not detectable in R450C urocanase extracts in a bacterial expression system. The unaffected father was heterozygous for R450C mutation, but DNA from the mother was unavailable for testing. Neither mutation was found in 200 ethnically matched control chromosomes."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "19304569", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "276880", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "UROC1"}], "names": [{"value": "UROC1, ARG450CYS"}], "variantType": "Variation", "otherNames": [{"value": "ARG450CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613012.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "UROCANASE DEFICIENCY (1 family)", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20582"}], "traitMappings": [{"medgens": [{"name": "Urocanate hydratase deficiency", "cui": "C0268514"}], "clinicalAssertionId": "20582", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "UROCANASE DEFICIENCY (1 family)", "mappingRef": "Preferred"}]}} -{"variationId": "221", "variationName": "NM_000027.4(AGA):c.916T>C (p.Cys306Arg)", 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"sequenceAccession": "NR_033655", "sequenceVersion": 2, "change": "n.902T>C"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001619", "type": "non-coding transcript variant"}], "type": "HGVS_TYPE_NON_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA114057"}, {"db": "UniProtKB", "id": "P20933#VAR_005075"}, {"db": "OMIM", "id": "613228.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "121964906", "type": "rs"}], "alleleId": "15260", "variationId": "221"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Aspartylglucosaminuria", "db": "MedGen", "id": "C0268225"}], "traitSetId": "72"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2023-04-10T00:00:00Z", "submissionCount": 2}}}, "title": "NM_000027.4(AGA):c.916T>C (p.Cys306Arg) AND Aspartylglucosaminuria", "accession": "RCV000000245", "version": 6}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "1722323", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Aspartylglycosaminuria", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Aspartylglucosaminuria/622"}]}, {"value": "Aspartylglucos-aminuria", "type": "Alternate"}, {"value": "Aspartylglucos-amidase (AGA) deficiency", "type": "Alternate"}, {"value": "AGA deficiency", "type": "Alternate"}, {"value": "Glycosylasparaginase deficiency", "type": "Alternate"}, {"value": "GLYCOASPARAGINASE", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "208400", "type": "MIM"}]}, {"value": "Aspartylglucosaminuria", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0012068"}, {"db": "MONDO", "id": "MONDO:0008830"}]}], "symbols": [{"value": "AGU", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "208400", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "5854"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "5854"}]}], "xrefs": [{"db": "Orphanet", "id": "93"}, {"db": "MedGen", "id": "C0268225"}, {"db": "MONDO", "id": "MONDO:0008830"}, {"db": "OMIM", "id": "208400", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0012068", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "72", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2023-04-10T00:00:00Z", "dateCreated": "2015-07-12T00:00:00Z", "mostRecentSubmission": "2023-12-30T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613228.0003_ASPARTYLGLUCOSAMINURIA", "title": "AGA, CYS306ARG_ASPARTYLGLUCOSAMINURIA"}, "clinvarAccession": {"accession": "SCV000020389", "version": 4, "submitterIdentifiers": 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{"nucleotideExpression": {"expression": "NM_024884.2:c.164G>A", "sequenceAccessionVersion": "NM_024884.2", "sequenceAccession": "NM_024884", "sequenceVersion": 2, "change": "c.164G>A"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA115108"}, {"db": "UniProtKB", "id": "Q9H9P8#VAR_025682"}, {"db": "OMIM", "id": "609584.0004", "type": "Allelic variant"}, {"db": "dbSNP", "id": "118204021", "type": "rs"}], "alleleId": "16649", "variationId": "1610"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "L-2-hydroxyglutaric aciduria", "db": "MedGen", "id": "C1855995"}], "traitSetId": "414"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2004-11-15T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.164G>A (p.Gly55Asp) AND L-2-hydroxyglutaric aciduria", "accession": "RCV000001677", "version": 4}, {"classifiedConditionList": {"classifiedConditions": [{"value": "L2HGDH-related condition"}], "traitSetId": "90824"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2024-01-30T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.164G>A (p.Gly55Asp) AND L2HGDH-related condition", "accession": "RCV003398413", "version": 5}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "15385440", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "L2HGDH-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE", "id": "90824", "contributesToAggregateClassification": true}, {"traits": [{"names": 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"numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "609584.0004_L-2-HYDROXYGLUTARIC ACIDURIA", "title": "L2HGDH, GLY55ASP_L-2-HYDROXYGLUTARIC ACIDURIA"}, "clinvarAccession": {"accession": "SCV000021833", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-11-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2004-11-15T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In members of 3 consanguineous Turkish families with L-2-hydroxyglutaric aciduria (L2HGA; 236792), Topcu et al. (2004) described homozygosity for a 164G-A transition in exon 2 of the L2HGDH gene, which was predicted to result in a substitution of aspartic acid for glycine at residue 55 (G55D)."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "15385440", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "names": [{"value": "L2HGDH, GLY55ASP"}], "variantType": "Variation", "otherNames": [{"value": "GLY55ASP", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "609584.0004", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "L-2-HYDROXYGLUTARIC ACIDURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21833"}, {"clinvarSubmissionId": {"localKey": "37587525|L2HGDH-related condition", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004103622", "version": 2, "submitterIdentifiers": {"submitterName": "PreventionGenetics, part of Exact Sciences", "orgId": "239772", "orgCategory": "laboratory", "orgAbbreviation": "PG"}, "dateUpdated": "2024-03-16T00:00:00Z", "dateCreated": "2023-11-20T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "The L2HGDH c.164G>A variant is predicted to result in the amino acid substitution p.Gly55Asp. This variant was reported in the homozygous state in four individuals from three families; all individuals had biochemically confirmed L-2-Hydroxyglutaric aciduria (Topcu et al. 2004. PubMed ID: 15385440). It was also reported in the compound heterozygous state with a pathogenic frameshift variant in two affected relatives (Sass et al. 2008. PubMed ID: 18415700). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as likely pathogenic."}], "dateLastEvaluated": "2024-01-30T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_024884.2:c.164G>A"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "L2HGDH-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB13915440", "SUB14299258"], "id": "7685222"}], "traitMappings": [{"medgens": [{"name": "L-2-hydroxyglutaric 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{"classifiedConditionList": {"classifiedConditions": [{"value": "FRZB-related condition"}], "traitSetId": "95598"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Benign", "dateLastEvaluated": "2019-12-03T00:00:00Z", "submissionCount": 1}}}, "title": "NM_001463.4(FRZB):c.970C>G (p.Arg324Gly) AND FRZB-related condition", "accession": "RCV003964794", "version": 1}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Benign", "citations": [{"ids": [{"value": "15210948", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "FRZB-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE", "id": "95598", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "Osteoarthritis", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0002758"}, {"db": "MONDO", "id": "MONDO:0005178"}]}, {"value": "OSTEOARTHROSIS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "165720", "type": "MIM"}]}], "symbols": [{"value": "OA", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "165720", "type": "MIM"}]}], "citations": [{"url": "https://www.nice.org.uk/guidance/ng226", "citationText": "UK NICE Guideline NG226, Osteoarthritis in over 16s: diagnosis and management, 2022", "type": "practice guideline", "abbrev": "NICE, 2022"}, {"url": "https://www.nice.org.uk/guidance/ng193", "citationText": "UK NICE Guideline NG193, Chronic pain (primary and secondary) in over 16s: assessment of all chronic pain and management of chronic primary pain, 2021", "type": "practice guideline", "abbrev": "NICE, 2021"}], "xrefs": [{"db": "MedGen", "id": "C0029408"}, {"db": "MONDO", "id": "MONDO:0005178"}, {"db": "Human Phenotype Ontology", "id": "HP:0002758", "type": "primary"}, {"db": "Human Phenotype 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The association was confirmed in an independent cohort of female hip cases (p = 0.04)."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "15210948", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "165720", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "FRZB"}], "names": [{"value": "FRZB, ARG324GLY"}], "variantType": "Variation", "otherNames": [{"value": "ARG324GLY", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "605083.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "OSTEOARTHRITIS SUSCEPTIBILITY 1", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "25712"}, {"clinvarSubmissionId": {"localKey": "388831|FRZB-related condition", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004778771", "version": 1, "submitterIdentifiers": {"submitterName": "PreventionGenetics, part of Exact Sciences", "orgId": "239772", "orgCategory": "laboratory", "orgAbbreviation": "PG"}, "dateUpdated": 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Testicular descent from abdomen to scrotum occurs in 2 distinct phases: the transabdominal phase and the inguinoscrotal phase (summary by Gorlov et al., 2002)."}, "type": "public definition"}, "xrefs": [{"db": "OMIM", "id": "219050", "type": "MIM"}]}], "xrefs": [{"db": "MedGen", "id": "C0010417"}, {"db": "MONDO", "id": "MONDO:0009047"}, {"db": "OMIM", "id": "219050", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0000028", "type": "primary"}, {"db": "Human Phenotype Ontology", "id": "HP:0000797", "type": "secondary"}]}], "type": "TYPE_DISEASE", "id": "1141", "contributesToAggregateClassification": false}], "dateLastEvaluated": "2022-11-01T00:00:00Z", "dateCreated": "2015-08-16T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "606655.0001_RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "title": "RXFP2, THR222PRO_RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE"}, "clinvarAccession": {"accession": "SCV000024548", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-08-16T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Uncertain significance", "dateLastEvaluated": "2011-08-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "This variant, formerly titled CRYPTORCHIDISM (see 219050), has been reclassified based on the findings of Ars et al. 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(2010) concluded that T222P is a frequent variant in the Spanish population with no pathogenic effect, although the variant seemed to confer a mild risk for cryptorchidism in the Italian population. The authors stated that these data exclude a clear-cut cause-effect relationship between the T222P variant and testicular maldescent."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20636340", "source": "PubMed"}]}]}]}], "simpleAllele": {"genes": [{"symbol": "RXFP2"}], "names": [{"value": "RXFP2, THR222PRO"}], "variantType": "Variation", "otherNames": [{"value": "THR222PRO", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "606655.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "24548"}, {"clinvarSubmissionId": {"localKey": "134119|MedGen:CN517202", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004132958", "version": 4, "submitterIdentifiers": {"submitterName": "CeGaT Center for Human Genetics Tuebingen", "orgId": "505870", "orgCategory": "laboratory", "orgAbbreviation": "CHGT"}, "dateUpdated": "2024-04-15T00:00:00Z", "dateCreated": "2023-11-20T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely benign", "comments": [{"value": "RXFP2: BP4, BS2"}], "dateLastEvaluated": "2022-11-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/api/2.0/files/0ynenhfo/cegat_center_for_human_genetics_tuebingen_-_variant_classification_criteria_-_version_2.pdf/?format=attachment"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_ALLELES"}]}]}], "simpleAllele": {"genes": [{"symbol": "RXFP2"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_13", "start": 32351535, "stop": 32351535, "variantLength": 1, "referenceAllele": "A", "alternateAllele": "C"}]}}, "traitSet": {"traits": [{"xrefs": [{"db": "MedGen", "id": "CN517202", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["2024-04", "SUB13985080", "SUB14102099", "SUB14290090"], "id": "7709681"}], "traitMappings": [{"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "7709681", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Breast-ovarian cancer, familial, susceptibility to, 2", "cui": "C2675520"}], "clinicalAssertionId": "24548", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "mappingRef": "Preferred"}]}} -{"variationId": "1212", "variationName": "GNAS, 4.7-KB DEL", "variationType": "Deletion", "dateCreated": "2013-04-04T00:00:00Z", "dateLastUpdated": "2024-05-01T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "accession": "VCV000001212", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["20q13.32"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 58839748, "stop": 58911192, "displayStart": 58839748, "displayStop": 58911192, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_20", "accession": "NC_000020.10", "start": 57414794, "stop": 57486249, "displayStart": 57414794, "displayStop": 57486249, "strand": "+"}]}], "omims": ["139320"], "haploinsufficiency": {"value": "Sufficient evidence for dosage pathogenicity", "lastEvaluated": "2021-01-12T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=GNAS"}, "triplosensitivity": {"value": "No evidence available", "lastEvaluated": "2021-01-12T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=GNAS"}, "fullName": "GNAS complex locus", "geneId": "2778", "hgncId": "HGNC:4392", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED"}, {"locations": [{"cytogeneticLocations": ["20q13.32"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 58818918, "stop": 58850902, "displayStart": 58818918, "displayStop": 58850902, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_20", "accession": "NC_000020.10", "start": 57393972, "stop": 57425957, "displayStart": 57393972, "displayStop": 57425957, "strand": "-"}]}], "omims": ["610540"], "fullName": "GNAS antisense RNA 1", "geneId": "149775", "hgncId": "HGNC:24872", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED"}], "name": "GNAS, 4.7-KB DEL", "variantTypes": ["Deletion"], "locations": [{"cytogeneticLocations": ["20q13.2"]}], "otherNames": [{"value": "4.7-KB DEL"}], "xrefs": [{"db": "OMIM", "id": "139320.0031", "type": "Allelic variant"}, {"db": "OMIM", "id": "610540.0001", "type": "Allelic variant"}], "alleleId": "16251", "variationId": "1212"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Pseudohypoparathyroidism type 1B", "db": "MedGen", "id": "C1864100"}], "traitSetId": "321"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2005-01-01T00:00:00Z", "submissionCount": 1}}}, "title": "GNAS, 4.7-KB DEL AND Pseudohypoparathyroidism type 1B", "accession": "RCV000001271", "version": 9}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "15592469", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Pseudohypoparathyroidism Type IB", "type": "Alternate"}, {"value": "Pseudohypoparathyroidism type 1B", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "Pseudohypoparathyroidism+type+1B/6036"}, {"db": "MONDO", "id": "MONDO:0011301"}]}, {"value": "PHP IB", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}], "symbols": [{"value": "PHP1B", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "Disorders of GNAS inactivation include the phenotypes pseudohypoparathyroidism Ia, Ib, and Ic (PHP-Ia, -Ib, -Ic), pseudopseudohypoparathyroidism (PPHP), progressive osseous heteroplasia (POH), and osteoma cutis (OC). PHP-Ia and PHP-Ic are characterized by: End-organ resistance to endocrine hormones including parathyroid hormone (PTH), thyroid-stimulating hormone (TSH), gonadotropins (LH and FSH), growth hormone-releasing hormone (GHRH), and CNS neurotransmitters (leading to obesity and variable degrees of intellectual disability and developmental delay); and The Albright hereditary osteodystrophy (AHO) phenotype (short stature, round facies, and subcutaneous ossifications) and brachydactyly type E (shortening mainly of the 4th and/or 5th metacarpals and metatarsals and distal phalanx of the thumb). Although PHP-Ib is characterized principally by PTH resistance, some individuals also have partial TSH resistance and mild features of AHO (e.g., brachydactyly). PPHP, a more limited form of PHP-Ia, is characterized by various manifestations of the AHO phenotype without the hormone resistance or obesity. POH and OC are even more restricted variants of PPHP: POH consists of dermal ossification beginning in infancy, followed by increasing and extensive bone formation in deep muscle and fascia. OC consists of extra-skeletal ossification that is limited to the dermis and subcutaneous tissues."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK459117"}]}, {"attribute": {"base": {"integerValue": "10680"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10680"}]}], "citations": [{"ids": [{"value": "29072892", "source": "PubMed"}, {"value": "NBK459117", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "94089"}, {"db": "MedGen", "id": "C1864100"}, {"db": "MONDO", "id": "MONDO:0011301"}, {"db": "OMIM", "id": "603233", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "321", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2005-01-01T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "610540.0001_PSEUDOHYPOPARATHYROIDISM, TYPE IB", "title": "GNASAS, 4.7-KB DEL _PSEUDOHYPOPARATHYROIDISM, TYPE IB"}, "clinvarAccession": {"accession": "SCV000021421", "version": 1, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2013-04-04T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2005-01-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 unrelated kindreds with pseudohypoparathyroidism type Ib (603233), Bastepe et al. 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When inherited from a female, the deletion abolished all maternal GNAS imprints and derepressed maternally silenced transcripts, suggesting that the deleted region contains a cis-acting element that controls imprinting of the maternal GNAS allele."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "15592469", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "GNASAS"}], "names": [{"value": "GNASAS, 4.7-KB DEL"}], "variantType": "Variation", "otherNames": [{"value": "4.7-KB DEL", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "610540.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "PSEUDOHYPOPARATHYROIDISM, TYPE IB", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21421"}], "traitMappings": [{"medgens": [{"name": "Pseudohypoparathyroidism type 1B", "cui": "C1864100"}], "clinicalAssertionId": "21421", "traitType": "Disease", "mappingType": 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"SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NR_033655.2:n.890G>A", "sequenceAccessionVersion": "NR_033655.2", "sequenceAccession": "NR_033655", "sequenceVersion": 2, "change": "n.890G>A"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001619", "type": "non-coding transcript variant"}], "type": "HGVS_TYPE_NON_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA114056"}, {"db": "UniProtKB", "id": "P20933#VAR_005074"}, {"db": "OMIM", "id": "613228.0002", "type": "Allelic variant"}, {"db": "dbSNP", "id": "121964905", "type": "rs"}], "alleleId": "15259", "variationId": "220"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Aspartylglucosaminuria", "db": "MedGen", "id": "C0268225"}], "traitSetId": "72"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "1991-12-15T00:00:00Z", "submissionCount": 1}}}, "title": "NM_000027.4(AGA):c.904G>A (p.Gly302Arg) AND Aspartylglucosaminuria", "accession": "RCV000000244", "version": 5}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "1722323", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Aspartylglucosaminuria", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0012068"}, {"db": "MONDO", "id": "MONDO:0008830"}]}, {"value": "Aspartylglycosaminuria", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Aspartylglucosaminuria/622"}]}, {"value": "Aspartylglucos-aminuria", "type": "Alternate"}, {"value": "Aspartylglucos-amidase (AGA) deficiency", "type": "Alternate"}, {"value": "AGA deficiency", "type": "Alternate"}, {"value": "Glycosylasparaginase 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"613228.0002_ASPARTYLGLUCOSAMINURIA", "title": "AGA, GLY302ARG_ASPARTYLGLUCOSAMINURIA"}, "clinvarAccession": {"accession": "SCV000020388", "version": 4, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-07-12T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "1991-12-15T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In a 10-year-old Turkish child with aspartylglucosaminuria (AGU; 208400), Ikonen et al. (1991) found a G-to-A substitution at nucleotide 904 of the AGA gene, resulting in substitution of arginine for glycine-302 (G302R). The patient was homozygous for the mutation and showed fibroblast AGA activity about 7% of normal. The parents were first cousins."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "1722323", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "208400", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "AGA"}], "name": {"value": "AGA, GLY302ARG"}, "variantType": "Variation", "otherNames": [{"value": "GLY302ARG", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613228.0002", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "ASPARTYLGLUCOSAMINURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20388"}], "traitMappings": [{"medgens": [{"name": "Aspartylglucosaminuria", "cui": "C0268225"}], "clinicalAssertionId": "20388", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "ASPARTYLGLUCOSAMINURIA", "mappingRef": "Preferred"}]}} +{"variationId": "224", "variationName": "NM_000027.4(AGA):c.102_108del (p.Thr33_Trp34insTer)", "variationType": "Deletion", "dateCreated": "2013-07-24T00:00:00Z", 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"name": "NM_024884.3(L2HGDH):c.293A>G (p.His98Arg)", "canonicalSpdi": "NC_000014.9:50302131:T:C", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["14q21.3"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_14", "accession": "NC_000014.9", "start": 50302132, "stop": 50302132, "displayStart": 50302132, "displayStop": 50302132, "variantLength": 1, "positionVcf": 50302132, "referenceAlleleVcf": "T", "alternateAlleleVcf": "C"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_14", "accession": "NC_000014.8", "start": 50768850, "stop": 50768850, "displayStart": 50768850, "displayStop": 50768850, "variantLength": 1, "positionVcf": 50768850, "referenceAlleleVcf": "T", "alternateAlleleVcf": "C"}]}], "otherNames": [{"value": "L2HGDH, HIS98ARG"}], "proteinChanges": ["H98R"], "hgvsExpressions": [{"proteinExpression": {"expression": "Q9H9P8:p.His98Arg", "sequenceAccessionVersion": "Q9H9P8", "sequenceAccession": "Q9H9P8", "change": "p.His98Arg"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "NC_000014.8:g.50768850T>C", "sequenceAccessionVersion": "NC_000014.8", "sequenceAccession": "NC_000014", "sequenceVersion": 8, "change": "g.50768850T>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000014.9:g.50302132T>C", "sequenceAccessionVersion": "NC_000014.9", "sequenceAccession": "NC_000014", "sequenceVersion": 9, "change": "g.50302132T>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_008092.1:g.15098A>G", "sequenceAccessionVersion": "NG_008092.1", "sequenceAccession": "NG_008092", "sequenceVersion": 1, "change": "g.15098A>G"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_024884.3:c.293A>G", "sequenceAccessionVersion": "NM_024884.3", "sequenceAccession": "NM_024884", "sequenceVersion": 3, "change": "c.293A>G", "maneSelect": true}, "proteinExpression": {"expression": "NP_079160.1:p.His98Arg", "sequenceAccessionVersion": "NP_079160.1", "sequenceAccession": "NP_079160", "sequenceVersion": 1, "change": "p.His98Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA115109"}, {"db": "UniProtKB", "id": "Q9H9P8#VAR_025685"}, {"db": "OMIM", "id": "609584.0006", "type": "Allelic variant"}, {"db": "dbSNP", "id": "267607206", "type": "rs"}], "alleleId": "16651", "variationId": "1612"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "L-2-hydroxyglutaric aciduria", "db": "MedGen", "id": "C1855995"}], "traitSetId": "414"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2010-01-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.293A>G (p.His98Arg) AND L-2-hydroxyglutaric aciduria", "accession": "RCV000001679", "version": 4}, {"classifiedConditionList": {"classifiedConditions": [{"value": "not provided", "db": "MedGen", "id": "CN517202"}], "traitSetId": "9460"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2017-10-05T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.293A>G (p.His98Arg) AND not provided", "accession": "RCV000522298", "version": 1}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "19911013", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "not provided", "type": "Preferred", "xrefs": [{"db": "Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre", "id": "13DG0619"}]}, {"value": "none provided", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"value": "The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."}, "type": "public definition"}}], "xrefs": [{"db": "MedGen", "id": "CN517202"}]}], "type": "TYPE_DISEASE", "id": "9460", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "L-2-hydroxyglutaric aciduria", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "L-2-hydroxyglutaric+aciduria/4061"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144"}, {"db": "MONDO", "id": "MONDO:0009370"}]}], "symbols": [{"value": "L2HGA", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "10472"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10472"}]}], "xrefs": [{"db": "Orphanet", "id": "79314"}, {"db": "MedGen", "id": "C1855995"}, {"db": "MONDO", "id": "MONDO:0009370"}, {"db": "OMIM", "id": "236792", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "414"}], "dateLastEvaluated": "2017-10-05T00:00:00Z", "dateCreated": "2017-11-10T00:00:00Z", "mostRecentSubmission": "2017-12-19T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "609584.0006_L-2-HYDROXYGLUTARIC ACIDURIA", "title": "L2HGDH, HIS98ARG_L-2-HYDROXYGLUTARIC ACIDURIA"}, "clinvarAccession": {"accession": "SCV000021835", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-11-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-01-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 unrelated Portuguese patients with L-2-hydroxyglutaric aciduria (L2HGA; 236792), Vilarinho et al. (2010) identified a homozygous 293A-G transition in the L2HGDH gene, resulting in a his98-to-arg (H98R) substitution in a conserved residue."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "19911013", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "name": {"value": "L2HGDH, HIS98ARG"}, "variantType": "Variation", "otherNames": [{"value": "HIS98ARG", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "609584.0006", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "L-2-HYDROXYGLUTARIC ACIDURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21835"}, {"clinvarSubmissionId": {"localKey": "GDX:742576|Not Provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV000617755", "version": 2, "submitterIdentifiers": {"submitterName": "GeneDx", "orgId": "26957", "orgCategory": "laboratory"}, "dateUpdated": "2017-12-19T00:00:00Z", "dateCreated": "2017-12-19T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "The H98R variant in the L2HGDH gene has been reported previously in the heterozygous state, in the presence of a second L2HGDH variant, and in the homozygous state, in multiple unrelated individuals with L-2-hydroxyglutaric aciduria, intellectual disability, and leukodystrophy (Vilarinho et al., 2005; Vilarinho et al., 2010). A different missense variant at the same residue, H98Y, has also been reported in the homozygous state in individuals with L-2-hydroxyglutaric aciduria (Top\u00c3\u00a7u et al., 2004; Haliloglu et al., 2008). The H98R variant is not observed in large population cohorts (Lek et al., 2016). The H98R variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret H98R as a likely pathogenic variant."}], "dateLastEvaluated": "2017-10-05T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "GeneDx Variant Classification (06012015)"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/dhtz9flo/genedx_interprules_final_061215.pdf"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_14", "start": 50768850, "stop": 50768850, "variantLength": 1, "referenceAllele": "T", "alternateAllele": "C"}]}, "attributes": [{"attribute": {"base": {"value": "NM_024884.2:c.293A>G"}, "type": "HGVS"}}]}, 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a 19-year-old Spanish woman with urocanic aciduria, mental retardation, and ataxia (UROCD; 276880), Espinos et al. (2009) identified compound heterozygosity for a 1348C-T transition in exon 14 of the UROC1 gene, resulting in an arg450-to-cys (R450C) substitution at a highly conserved residue, and a 209T-C transition in exon 2 (613012.0002), resulting in a leu70to-pro (L70P) substitution in the N-terminal alpha helix. Both mutations were predicted to have a pathologic effect, and enzyme activity was not detectable in R450C urocanase extracts in a bacterial expression system. The unaffected father was heterozygous for R450C mutation, but DNA from the mother was unavailable for testing. Neither mutation was found in 200 ethnically matched control chromosomes."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "19304569", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "276880", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "UROC1"}], "name": {"value": "UROC1, ARG450CYS"}, "variantType": "Variation", "otherNames": [{"value": "ARG450CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613012.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "UROCANASE DEFICIENCY (1 family)", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20582"}], "traitMappings": [{"medgens": [{"name": "Urocanate hydratase deficiency", "cui": "C0268514"}], "clinicalAssertionId": "20582", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "UROCANASE DEFICIENCY (1 family)", "mappingRef": "Preferred"}]}} +{"variationId": "221", "variationName": "NM_000027.4(AGA):c.916T>C (p.Cys306Arg)", 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"sequenceVersion": 4, "change": "c.916T>C", "maneSelect": true}, "proteinExpression": {"expression": "NP_000018.2:p.Cys306Arg", "sequenceAccessionVersion": "NP_000018.2", "sequenceAccession": "NP_000018", "sequenceVersion": 2, "change": "p.Cys306Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_001171988.2:c.886T>C", "sequenceAccessionVersion": "NM_001171988.2", "sequenceAccession": "NM_001171988", "sequenceVersion": 2, "change": "c.886T>C"}, "proteinExpression": {"expression": "NP_001165459.1:p.Cys296Arg", "sequenceAccessionVersion": "NP_001165459.1", "sequenceAccession": "NP_001165459", "sequenceVersion": 1, "change": "p.Cys296Arg"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NR_033655.2:n.902T>C", "sequenceAccessionVersion": "NR_033655.2", "sequenceAccession": "NR_033655", "sequenceVersion": 2, "change": "n.902T>C"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001619", "type": "non-coding transcript variant"}], "type": "HGVS_TYPE_NON_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA114057"}, {"db": "UniProtKB", "id": "P20933#VAR_005075"}, {"db": "OMIM", "id": "613228.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "121964906", "type": "rs"}], "alleleId": "15260", "variationId": "221"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Aspartylglucosaminuria", "db": "MedGen", "id": "C0268225"}], "traitSetId": "72"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2023-04-10T00:00:00Z", "submissionCount": 2}}}, "title": "NM_000027.4(AGA):c.916T>C (p.Cys306Arg) AND Aspartylglucosaminuria", "accession": "RCV000000245", "version": 6}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "1722323", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Aspartylglycosaminuria", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Aspartylglucosaminuria/622"}]}, {"value": "Aspartylglucos-aminuria", "type": "Alternate"}, {"value": "Aspartylglucos-amidase (AGA) deficiency", "type": "Alternate"}, {"value": "AGA deficiency", "type": "Alternate"}, {"value": "Glycosylasparaginase deficiency", "type": "Alternate"}, {"value": "GLYCOASPARAGINASE", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "208400", "type": "MIM"}]}, {"value": "Aspartylglucosaminuria", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0012068"}, {"db": "MONDO", "id": "MONDO:0008830"}]}], "symbols": 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{"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-07-12T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "1991-12-15T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In a 16-year-old white American patient with aspartylglucosaminuria (AGU; 208400), Ikonen et al. (1991) found by the SSCP method a T-to-C change at nucleotide 916 of the AGA gene, resulting in substitution of arginine for cysteine-306 (C306R)."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "1722323", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "208400", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "AGA"}], "name": {"value": "AGA, CYS306ARG"}, "variantType": "Variation", "otherNames": [{"value": "CYS306ARG", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613228.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "ASPARTYLGLUCOSAMINURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20389"}, {"clinvarSubmissionId": {"localKey": "NM_000027.4:c.916T>C|OMIM:208400", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004212573", "version": 1, "submitterIdentifiers": {"submitterName": "Baylor Genetics", "orgId": "1006", "orgCategory": "laboratory"}, "dateUpdated": 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"GRCh37"}, {"nucleotideExpression": {"expression": "NC_000014.9:g.50302994C>T", "sequenceAccessionVersion": "NC_000014.9", "sequenceAccession": "NC_000014", "sequenceVersion": 9, "change": "g.50302994C>T"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_008092.1:g.14236G>A", "sequenceAccessionVersion": "NG_008092.1", "sequenceAccession": "NG_008092", "sequenceVersion": 1, "change": "g.14236G>A"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_024884.3:c.164G>A", "sequenceAccessionVersion": "NM_024884.3", "sequenceAccession": "NM_024884", "sequenceVersion": 3, "change": "c.164G>A", "maneSelect": true}, "proteinExpression": {"expression": "NP_079160.1:p.Gly55Asp", "sequenceAccessionVersion": "NP_079160.1", "sequenceAccession": "NP_079160", "sequenceVersion": 1, "change": "p.Gly55Asp"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_024884.2:c.164G>A", "sequenceAccessionVersion": "NM_024884.2", "sequenceAccession": "NM_024884", "sequenceVersion": 2, "change": "c.164G>A"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA115108"}, {"db": "UniProtKB", "id": "Q9H9P8#VAR_025682"}, {"db": "OMIM", "id": "609584.0004", "type": "Allelic variant"}, {"db": "dbSNP", "id": "118204021", "type": "rs"}], "alleleId": "16649", "variationId": "1610"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "L-2-hydroxyglutaric aciduria", "db": "MedGen", "id": "C1855995"}], "traitSetId": "414"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2004-11-15T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.164G>A (p.Gly55Asp) AND L-2-hydroxyglutaric aciduria", "accession": "RCV000001677", "version": 4}, {"classifiedConditionList": {"classifiedConditions": [{"value": "L2HGDH-related condition"}], "traitSetId": "90824"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely pathogenic", "dateLastEvaluated": "2024-01-30T00:00:00Z", "submissionCount": 1}}}, "title": "NM_024884.3(L2HGDH):c.164G>A (p.Gly55Asp) AND L2HGDH-related condition", "accession": "RCV003398413", "version": 5}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely pathogenic", "citations": [{"ids": [{"value": "15385440", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "L2HGDH-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE", "id": "90824", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "L-2-hydroxyglutaric aciduria", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "L-2-hydroxyglutaric+aciduria/4061"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144"}, {"db": "MONDO", "id": "MONDO:0009370"}]}], "symbols": [{"value": "L2HGA", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"integerValue": "10472"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10472"}]}], "xrefs": [{"db": "Orphanet", "id": "79314"}, {"db": "MedGen", "id": "C1855995"}, {"db": "MONDO", "id": "MONDO:0009370"}, {"db": "OMIM", "id": "236792", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0040144", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "414", "contributesToAggregateClassification": false}], "dateLastEvaluated": "2024-01-30T00:00:00Z", "dateCreated": "2017-11-10T00:00:00Z", "mostRecentSubmission": "2024-03-16T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "609584.0004_L-2-HYDROXYGLUTARIC ACIDURIA", "title": "L2HGDH, GLY55ASP_L-2-HYDROXYGLUTARIC ACIDURIA"}, "clinvarAccession": {"accession": "SCV000021833", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-11-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2004-11-15T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In members of 3 consanguineous Turkish families with L-2-hydroxyglutaric aciduria (L2HGA; 236792), Topcu et al. (2004) described homozygosity for a 164G-A transition in exon 2 of the L2HGDH gene, which was predicted to result in a substitution of aspartic acid for glycine at residue 55 (G55D)."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "15385440", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "236792", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "name": {"value": "L2HGDH, GLY55ASP"}, "variantType": "Variation", "otherNames": [{"value": "GLY55ASP", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "609584.0004", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "L-2-HYDROXYGLUTARIC ACIDURIA", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21833"}, {"clinvarSubmissionId": {"localKey": "37587525|L2HGDH-related condition", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004103622", "version": 2, "submitterIdentifiers": {"submitterName": "PreventionGenetics, part of Exact Sciences", "orgId": "239772", "orgCategory": "laboratory", "orgAbbreviation": "PG"}, "dateUpdated": "2024-03-16T00:00:00Z", "dateCreated": "2023-11-20T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "The L2HGDH c.164G>A variant is predicted to result in the amino acid substitution p.Gly55Asp. This variant was reported in the homozygous state in four individuals from three families; all individuals had biochemically confirmed L-2-Hydroxyglutaric aciduria (Topcu et al. 2004. PubMed ID: 15385440). It was also reported in the compound heterozygous state with a pathogenic frameshift variant in two affected relatives (Sass et al. 2008. PubMed ID: 18415700). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as likely pathogenic."}], "dateLastEvaluated": "2024-01-30T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "L2HGDH"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_024884.2:c.164G>A"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "L2HGDH-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB13915440", "SUB14299258"], "id": "7685222"}], "traitMappings": [{"medgens": [{"name": "L-2-hydroxyglutaric 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"type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Reduced coagulation factor V activity", "type": "Alternate", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0003225"}]}, {"value": "Factor V deficiency", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "Factor+V+Deficiency/2709"}, {"db": "Human Phenotype Ontology", "id": "HP:0003225"}, {"db": "MONDO", "id": "MONDO:0020586"}, {"db": "SNOMED CT", "id": "4320005"}]}], "attributes": [{"attribute": {"base": {"value": "Factor V Leiden thrombophilia is characterized by a poor anticoagulant response to activated protein C (APC) and an increased risk for venous thromboembolism (VTE). Deep vein thrombosis (DVT) is the most common VTE, with the legs being the most common site. Thrombosis in unusual locations is less common. Evidence suggests that heterozygosity for the Leiden variant has at most a modest effect on risk for recurrent thrombosis after initial treatment of a first VTE. It is unlikely that factor V Leiden thrombophilia (i.e., heterozygosity or homozygosity for the Leiden variant) is a major factor contributing to pregnancy loss and other adverse pregnancy outcomes (preeclampsia, fetal growth restriction, and placental abruption). The clinical expression of factor V Leiden thrombophilia is influenced by the following: The number of Leiden variants (heterozygotes have a slightly increased risk for venous thrombosis; homozygotes have a much greater thrombotic risk). Coexisting genetic thrombophilic disorders, which have a supra-additive effect on overall thrombotic risk. Acquired thrombophilic disorders: antiphospholipid antibody (APLA) syndrome, paroxysmal nocturnal hemoglobinuria, myeloproliferative disorders, and increased levels of clotting factors. Circumstantial risk factors including but not limited to pregnancy, central venous catheters, travel, combined oral contraceptive (COC) use and other combined contraceptives, oral hormone replacement therapy (HRT), selective estrogen receptor modulators (SERMs), obesity, leg injury, and advancing age."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1368"}]}], "citations": [{"ids": [{"value": "20301542", "source": "PubMed"}, {"value": "NBK1368", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "21150787", "source": "PubMed"}], "type": "general", "abbrev": "EGAPP, 2011"}, {"ids": [{"value": "3111091", "source": "pmc"}], "type": "general", "abbrev": "Retired, ACMG, 2001"}, {"ids": [{"value": "33674767", "source": "PubMed"}], "type": "Suggested Reading", "abbrev": "ACMG, 2021"}, {"ids": [{"value": "35645034", "source": "PubMed"}], "type": "general", "abbrev": "BSH, 2022"}, {"url": "https://www.nice.org.uk/guidance/ng158", "citationText": "UK NICE Guideline NG158, Venous thromboembolic diseases: diagnosis, management and thrombophilia testing, 2023", "type": "practice guideline", "abbrev": "NICE, 2023"}], "xrefs": [{"db": "Orphanet", "id": "326"}, {"db": "MedGen", "id": "C4317320"}, {"db": "MONDO", "id": "MONDO:0020586"}, {"db": "Human Phenotype Ontology", "id": "HP:0003225", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "169", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2001-09-01T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "612309.0009_FACTOR V DEFICIENCY", "title": "F5, ARG1133TER_FACTOR V DEFICIENCY"}, "clinvarAccession": {"accession": "SCV000020835", "version": 1, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2013-04-04T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-09-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 seemingly unrelated southern Italian probands with undetectable plasma levels of factor V antigen and activity (227400), van Wijk et al. 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Acquired thrombophilic disorders: antiphospholipid antibody (APLA) syndrome, paroxysmal nocturnal hemoglobinuria, myeloproliferative disorders, and increased levels of clotting factors. Circumstantial risk factors including but not limited to pregnancy, central venous catheters, travel, combined oral contraceptive (COC) use and other combined contraceptives, oral hormone replacement therapy (HRT), selective estrogen receptor modulators (SERMs), obesity, leg injury, and advancing age."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1368"}]}], "citations": [{"ids": [{"value": "20301542", "source": "PubMed"}, {"value": "NBK1368", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "21150787", "source": "PubMed"}], "type": "general", "abbrev": "EGAPP, 2011"}, {"ids": [{"value": "3111091", "source": "pmc"}], "type": "general", "abbrev": "Retired, ACMG, 2001"}, {"ids": [{"value": "33674767", "source": "PubMed"}], "type": "Suggested Reading", "abbrev": "ACMG, 2021"}, {"ids": [{"value": "35645034", "source": "PubMed"}], "type": "general", "abbrev": "BSH, 2022"}, {"url": "https://www.nice.org.uk/guidance/ng158", "citationText": "UK NICE Guideline NG158, Venous thromboembolic diseases: diagnosis, management and thrombophilia testing, 2023", "type": "practice guideline", "abbrev": "NICE, 2023"}], "xrefs": [{"db": "Orphanet", "id": "326"}, {"db": "MedGen", "id": "C4317320"}, {"db": "MONDO", "id": "MONDO:0020586"}, {"db": "Human Phenotype Ontology", "id": "HP:0003225", "type": "primary"}]}], "type": "TYPE_DISEASE", "id": "169", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2019-02-01T00:00:00Z", "dateCreated": "2017-08-20T00:00:00Z", "mostRecentSubmission": "2019-09-29T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "612309.0012_FACTOR V DEFICIENCY", "title": "F5, ARG2074CYS_FACTOR V DEFICIENCY"}, "clinvarAccession": {"accession": "SCV000020838", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-08-20T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2003-01-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In a 22-year-old Italian woman in whom factor V deficiency (227400) was first diagnosed at the age of 10 years after abnormal coagulation screening tests were found preceding an operation for strabismus, Duga et al. 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"2011-08-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_130806.5(RXFP2):c.664A>C (p.Thr222Pro) AND Cryptorchidism", "accession": "RCV000004376", "version": 3}, {"classifiedConditionList": {"classifiedConditions": [{"value": "not provided", "db": "MedGen", "id": "C3661900"}], "traitSetId": "9460"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely benign", "dateLastEvaluated": "2022-11-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_130806.5(RXFP2):c.664A>C (p.Thr222Pro) AND not provided", "accession": "RCV003389746", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely benign", "citations": [{"ids": [{"value": "12217959", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "12970298", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "20636340", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "not provided", "type": "Preferred", "xrefs": [{"db": "Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre", "id": "13DG0619"}]}, {"value": "none provided", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"value": "The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."}, "type": "public definition"}}], "xrefs": [{"db": "MedGen", "id": "C3661900"}]}], "type": "TYPE_DISEASE", "id": "9460", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "undescended testicle", "type": "Alternate"}, {"value": "Cryptorchidism", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0000028"}, {"db": "MONDO", "id": "MONDO:0009047"}]}, {"value": "Cryptorchidism, unilateral or bilateral", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Cryptorchidism%2C+unilateral+or+bilateral/8117"}]}], "attributes": [{"attribute": {"base": {"value": "Cryptorchidism, or failure of testicular descent, is a common human congenital abnormality with a multifactorial etiology that likely reflects the involvement of endocrine, environmental, and hereditary factors. Cryptorchidism can result in infertility and increases risk for testicular tumors. Testicular descent from abdomen to scrotum occurs in 2 distinct phases: the transabdominal phase and the inguinoscrotal phase (summary by Gorlov et al., 2002)."}, "type": "public definition"}, "xrefs": [{"db": "OMIM", "id": "219050", "type": "MIM"}]}], "xrefs": [{"db": "MedGen", "id": "C0010417"}, {"db": "MONDO", "id": "MONDO:0009047"}, {"db": "OMIM", "id": "219050", "type": "MIM"}, {"db": "Human Phenotype Ontology", "id": "HP:0000028", "type": "primary"}, {"db": "Human Phenotype Ontology", "id": "HP:0000797", "type": "secondary"}]}], "type": "TYPE_DISEASE", "id": "1141", "contributesToAggregateClassification": false}], "dateLastEvaluated": "2022-11-01T00:00:00Z", "dateCreated": "2015-08-16T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "606655.0001_RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "title": "RXFP2, THR222PRO_RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE"}, "clinvarAccession": {"accession": "SCV000024548", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-08-16T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Uncertain significance", "dateLastEvaluated": "2011-08-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "This variant, formerly titled CRYPTORCHIDISM (see 219050), has been reclassified based on the findings of Ars et al. (2010)."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20636340", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "219050", "type": "MIM"}]}, {"attributes": [{"base": {"value": "By mutation screening of the LGR8 gene on DNA from 60 cryptorchid patients, Gorlov et al. (2002) identified a heterozygous thr222-to-pro (T222P) mutation in the ectodomain in 1 patient. The mutant receptor failed to respond to ligand stimulation, implicating LGR8 in the etiology of some cases of cryptorchidism in humans."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "12217959", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "By sequencing the LGR8 and INSL3 (146738) genes in a cohort of 87 patients with corrected cryptorchidism and 80 controls, Ferlin et al. (2003) identified the T222P mutation in LGR8 in 4 patients and 3 mutations in INSL3 (146738.0002-146738.0004) in 4 patients (8 of 87; 9.2%). The authors concluded that INSL3-LGR8 mutations are frequently associated with human cryptorchidism and are maternally inherited."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "12970298", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "146738", "type": "MIM"}]}, {"attributes": [{"base": {"value": "Ars et al. (2010) screened for the RXFP2 T222P variant in 577 Spanish men, including 187 with a history of cryptorchidism and 390 controls, and in 550 Italian men, including 199 with a history of cryptorchidism and 351 controls. In the Spanish study population, the T222P variant was present at similar frequency in both cases (3 of 187; 1.6%) and controls (7 of 390; 1.8%). In the Italian study population, the variant was significantly more frequent in cases (9 of 199; 4.5%) than in controls (5 of 351; 1.4%), with an odds ratio of 3.17 (p = 0.031). Ars et al. (2010) concluded that T222P is a frequent variant in the Spanish population with no pathogenic effect, although the variant seemed to confer a mild risk for cryptorchidism in the Italian population. The authors stated that these data exclude a clear-cut cause-effect relationship between the T222P variant and testicular maldescent."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20636340", "source": "PubMed"}]}]}]}], "simpleAllele": {"genes": [{"symbol": "RXFP2"}], "name": {"value": "RXFP2, THR222PRO"}, "variantType": "Variation", "otherNames": [{"value": "THR222PRO", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "606655.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "24548"}, {"clinvarSubmissionId": {"localKey": "134119|MedGen:CN517202", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004132958", "version": 4, "submitterIdentifiers": {"submitterName": "CeGaT Center for Human Genetics Tuebingen", "orgId": "505870", "orgCategory": "laboratory", "orgAbbreviation": "CHGT"}, "dateUpdated": "2024-04-15T00:00:00Z", "dateCreated": "2023-11-20T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely benign", "comments": [{"value": "RXFP2: BP4, BS2"}], "dateLastEvaluated": "2022-11-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/api/2.0/files/0ynenhfo/cegat_center_for_human_genetics_tuebingen_-_variant_classification_criteria_-_version_2.pdf/?format=attachment"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_ALLELES"}]}]}], "simpleAllele": {"genes": [{"symbol": "RXFP2"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_13", "start": 32351535, "stop": 32351535, "variantLength": 1, "referenceAllele": "A", "alternateAllele": "C"}]}}, "traitSet": {"traits": [{"xrefs": [{"db": "MedGen", "id": "CN517202", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["2024-04", "SUB13985080", "SUB14102099", "SUB14290090"], "id": "7709681"}], "traitMappings": [{"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "7709681", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Breast-ovarian cancer, familial, susceptibility to, 2", "cui": "C2675520"}], "clinicalAssertionId": "24548", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE", "mappingRef": "Preferred"}]}} +{"variationId": "1212", "variationName": "GNAS, 4.7-KB DEL", "variationType": "Deletion", "dateCreated": "2013-04-04T00:00:00Z", "dateLastUpdated": "2024-05-01T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "accession": "VCV000001212", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["20q13.32"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 58839748, "stop": 58911192, "displayStart": 58839748, "displayStop": 58911192, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_20", "accession": "NC_000020.10", "start": 57414794, "stop": 57486249, "displayStart": 57414794, "displayStop": 57486249, "strand": "+"}]}], "omims": ["139320"], "haploinsufficiency": {"value": "Sufficient evidence for dosage pathogenicity", "lastEvaluated": "2021-01-12T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=GNAS"}, "triplosensitivity": {"value": "No evidence available", "lastEvaluated": "2021-01-12T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=GNAS"}, "fullName": "GNAS complex locus", "geneId": "2778", "hgncId": "HGNC:4392", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED"}, {"locations": [{"cytogeneticLocations": ["20q13.32"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 58818918, "stop": 58850902, "displayStart": 58818918, "displayStop": 58850902, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_20", "accession": "NC_000020.10", "start": 57393972, "stop": 57425957, "displayStart": 57393972, "displayStop": 57425957, "strand": "-"}]}], "omims": ["610540"], "fullName": "GNAS antisense RNA 1", "geneId": "149775", "hgncId": "HGNC:24872", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED"}], "name": "GNAS, 4.7-KB DEL", "variantTypes": ["Deletion"], "locations": [{"cytogeneticLocations": ["20q13.2"]}], "otherNames": [{"value": "4.7-KB DEL"}], "xrefs": [{"db": "OMIM", "id": "139320.0031", "type": "Allelic variant"}, {"db": "OMIM", "id": "610540.0001", "type": "Allelic variant"}], "alleleId": "16251", "variationId": "1212"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Pseudohypoparathyroidism type 1B", "db": "MedGen", "id": "C1864100"}], "traitSetId": "321"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2005-01-01T00:00:00Z", "submissionCount": 1}}}, "title": "GNAS, 4.7-KB DEL AND Pseudohypoparathyroidism type 1B", "accession": "RCV000001271", "version": 9}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "15592469", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Pseudohypoparathyroidism Type IB", "type": "Alternate"}, {"value": "Pseudohypoparathyroidism type 1B", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "Pseudohypoparathyroidism+type+1B/6036"}, {"db": "MONDO", "id": "MONDO:0011301"}]}, {"value": "PHP IB", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}], "symbols": [{"value": "PHP1B", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "Disorders of GNAS inactivation include the phenotypes pseudohypoparathyroidism Ia, Ib, and Ic (PHP-Ia, -Ib, -Ic), pseudopseudohypoparathyroidism (PPHP), progressive osseous heteroplasia (POH), and osteoma cutis (OC). PHP-Ia and PHP-Ic are characterized by: End-organ resistance to endocrine hormones including parathyroid hormone (PTH), thyroid-stimulating hormone (TSH), gonadotropins (LH and FSH), growth hormone-releasing hormone (GHRH), and CNS neurotransmitters (leading to obesity and variable degrees of intellectual disability and developmental delay); and The Albright hereditary osteodystrophy (AHO) phenotype (short stature, round facies, and subcutaneous ossifications) and brachydactyly type E (shortening mainly of the 4th and/or 5th metacarpals and metatarsals and distal phalanx of the thumb). Although PHP-Ib is characterized principally by PTH resistance, some individuals also have partial TSH resistance and mild features of AHO (e.g., brachydactyly). PPHP, a more limited form of PHP-Ia, is characterized by various manifestations of the AHO phenotype without the hormone resistance or obesity. POH and OC are even more restricted variants of PPHP: POH consists of dermal ossification beginning in infancy, followed by increasing and extensive bone formation in deep muscle and fascia. OC consists of extra-skeletal ossification that is limited to the dermis and subcutaneous tissues."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK459117"}]}, {"attribute": {"base": {"integerValue": "10680"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10680"}]}], "citations": [{"ids": [{"value": "29072892", "source": "PubMed"}, {"value": "NBK459117", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "94089"}, {"db": "MedGen", "id": "C1864100"}, {"db": "MONDO", "id": "MONDO:0011301"}, {"db": "OMIM", "id": "603233", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "321", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2005-01-01T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "610540.0001_PSEUDOHYPOPARATHYROIDISM, TYPE IB", "title": "GNASAS, 4.7-KB DEL _PSEUDOHYPOPARATHYROIDISM, TYPE IB"}, "clinvarAccession": {"accession": "SCV000021421", "version": 1, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2013-04-04T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2005-01-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 unrelated kindreds with pseudohypoparathyroidism type Ib (603233), Bastepe et al. (2005) identified a 4.7-kb deletion that removed the differentially methylated region of the GNAS gene (139320.0031) encompassing the NESP55 region and exons 3 and 4 of the GNAS antisense transcript. When inherited from a female, the deletion abolished all maternal GNAS imprints and derepressed maternally silenced transcripts, suggesting that the deleted region contains a cis-acting element that controls imprinting of the maternal GNAS allele."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "15592469", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "603233", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "GNASAS"}], "name": {"value": "GNASAS, 4.7-KB DEL"}, "variantType": "Variation", "otherNames": [{"value": "4.7-KB DEL", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "610540.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "PSEUDOHYPOPARATHYROIDISM, TYPE IB", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "21421"}], "traitMappings": [{"medgens": [{"name": "Pseudohypoparathyroidism type 1B", "cui": "C1864100"}], "clinicalAssertionId": "21421", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "PSEUDOHYPOPARATHYROIDISM, TYPE IB", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/data/records_with_maf.jsonl b/tests/clinvar_data/data/records_with_maf.jsonl index 1003aad..ac2bf87 100644 --- a/tests/clinvar_data/data/records_with_maf.jsonl +++ b/tests/clinvar_data/data/records_with_maf.jsonl @@ -1,2 +1,2 @@ -{"variationId": "442", "variationName": "NM_005581.5(BCAM):c.711C>A (p.Cys237Ter)", "variationType": "single nucleotide variant", "dateCreated": "2018-02-08T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2018-02-08T00:00:00Z", "accession": "VCV000000442", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["19q13.32"], "sequenceLocations": [{"assembly": "GRCh38", "chr": 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44813547, "referenceAlleleVcf": "C", "alternateAlleleVcf": "A"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_19", "accession": "NC_000019.9", "start": 45316804, "stop": 45316804, "displayStart": 45316804, "displayStop": 45316804, "variantLength": 1, "positionVcf": 45316804, "referenceAlleleVcf": "C", "alternateAlleleVcf": "A"}]}], "proteinChanges": ["C237*"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "LRG_798:g.9467C>A", "sequenceAccessionVersion": "LRG_798", "sequenceAccession": "LRG_798"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_798t2:c.711C>A", "sequenceAccessionVersion": "LRG_798t2", "sequenceAccession": "LRG_798t2"}, "proteinExpression": {"expression": "LRG_798p2:p.Cys237Ter", "sequenceAccessionVersion": "LRG_798p2", "sequenceAccession": "LRG_798p2", "change": "p.Cys237Ter"}, "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NC_000019.10:g.44813547C>A", "sequenceAccessionVersion": "NC_000019.10", 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"p.Cys237Ter"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001587", "type": "nonsense"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_005581.5:c.711C>A", "sequenceAccessionVersion": "NM_005581.5", "sequenceAccession": "NM_005581", "sequenceVersion": 5, "change": "c.711C>A", "maneSelect": true}, "proteinExpression": {"expression": "NP_005572.2:p.Cys237Ter", "sequenceAccessionVersion": "NP_005572.2", "sequenceAccession": "NP_005572", "sequenceVersion": 2, "change": "p.Cys237Ter"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001587", "type": "nonsense"}], "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA114290"}, {"db": "OMIM", "id": "612773.0005", "type": "Allelic variant"}, {"db": "dbSNP", "id": "3810141", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.10004, "source": "1000 Genomes Project", "minorAllele": "T"}, "alleleId": "15481", "variationId": "442"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": 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9d12106..2f99a5b 100644 --- a/tests/clinvar_data/data/records_with_maf.xml +++ b/tests/clinvar_data/data/records_with_maf.xml @@ -179,7 +179,6 @@ - current Homo sapiens diff --git a/tests/clinvar_data/data/ten_records.jsonl b/tests/clinvar_data/data/ten_records.jsonl index 34ca9b0..eec7693 100644 --- a/tests/clinvar_data/data/ten_records.jsonl +++ b/tests/clinvar_data/data/ten_records.jsonl @@ -1,10 +1,10 @@ -{"variationId": "2", "variationName": "NM_014855.3(AP5Z1):c.80_83delinsTGCTGTAAACTGTAACTGTAAA (p.Arg27_Ile28delinsLeuLeuTer)", "variationType": "Indel", "dateCreated": "2017-01-30T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2021-05-16T00:00:00Z", "accession": "VCV000000002", "version": 3, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": 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"NP_001116423.1:p.Arg91Cys", "sequenceAccessionVersion": "NP_001116423.1", "sequenceAccession": "NP_001116423", "sequenceVersion": 1, "change": "p.Arg91Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_002036.4:c.265C>T", "sequenceAccessionVersion": "NM_002036.4", "sequenceAccession": "NM_002036", "sequenceVersion": 4, "change": "c.265C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_002027.2:p.Arg89Cys", "sequenceAccessionVersion": "NP_002027.2", "sequenceAccession": "NP_002027", "sequenceVersion": 2, "change": "p.Arg89Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"proteinExpression": {"expression": "Q16570:p.Arg89Cys", "sequenceAccessionVersion": "Q16570", "sequenceAccession": "Q16570", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "LRG_801:g.6692C>T", "sequenceAccessionVersion": "LRG_801", "sequenceAccession": "LRG_801"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_801t1:c.265C>T", "sequenceAccessionVersion": "LRG_801t1", "sequenceAccession": "LRG_801t1"}, "proteinExpression": {"expression": "LRG_801p1:p.Arg89Cys", "sequenceAccessionVersion": "LRG_801p1", "sequenceAccession": "LRG_801p1", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA113789"}, {"db": "UniProtKB", "id": "Q16570#VAR_015068"}, {"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "34599082", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.00459, "source": "1000 Genomes Project", "minorAllele": "T"}, "alleleId": "33435", "variationId": "18396"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}], "traitSetId": "6213"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys) AND DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "accession": "RCV000000009", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "11369664", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8547665", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9399903", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9731074", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9746760", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9886340", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}]}], "type": "TYPE_DISEASE", "id": "6213", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2001-06-01T00:00:00Z", "dateCreated": "2017-12-15T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613665.0003_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "title": "ACKR1, ARG89CYS_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}, "clinvarAccession": {"accession": "SCV000020152", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-12-15T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": 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(1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. They found that in some of these cases Fy(b-) individuals had the wildtype FY*B GATA but carried 271C-T and 304G-A mutations. The 271C-T substitution resulted in an R91C amino acid substitution (R89C in the predominant DARC isoform reported by Iwamoto et al. (1996)), which represented a considerable change of chemical nature, one that may affect the antigenic determinants of DARC, and thus may be of clinical significance. Parasol et al. (1998) noted that further studies were needed to determine whether erythrocytes carrying these mutations behave as Fy(bwk) variants."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9746760", "source": "PubMed"}]}, {"ids": [{"value": "8547665", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Carrington et al. (1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. (2001) showed that in both the CCR5 R60S and DARC R89C alleles, the loss of a positive charge from the intracellular loop leads to reduced surface expression, thereby identifying a novel mechanism that may be protective against disease: against malarial infection by Plasmodium vivax in the case of the DARC gene and against AIDS in the case of the CCR5 gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9399903", "source": "PubMed"}]}, {"ids": [{"value": "11369664", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "601373", "type": "MIM"}, {"db": "OMIM", "id": "609423", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "ACKR1"}], "names": [{"value": "ACKR1, ARG89CYS"}], "variantType": "Variation", "otherNames": [{"value": "ARG89CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred"}]}], "type": 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"description": {"value": "Pathogenic", "submissionCount": 2}}}, "title": "NM_014855.3(AP5Z1):c.80_83delinsTGCTGTAAACTGTAACTGTAAA (p.Arg27_Ile28delinsLeuLeuTer) AND Hereditary spastic paraplegia 48", "accession": "RCV000000012", "version": 5}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "citations": [{"ids": [{"value": "20613862", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "Hereditary spastic paraplegia 48", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0013342"}]}, {"value": "Spastic paraplegia 48", "type": "Alternate"}, {"value": "Spastic paraplegia 48, autosomal recessive", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Spastic+paraplegia+48%2C+autosomal+recessive/9323"}]}], "symbols": [{"value": "SPG48", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "613647", "type": "MIM"}]}], "xrefs": [{"db": "Orphanet", "id": "306511"}, {"db": "MedGen", "id": "C3150901"}, {"db": "MONDO", "id": "MONDO:0013342"}, {"db": "OMIM", "id": "613647", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "2", "contributesToAggregateClassification": true}], "dateCreated": "2017-01-30T00:00:00Z", "mostRecentSubmission": "2021-05-16T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613653.0001_SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE", "title": "AP5Z1, 4-BP DEL/22-BP INS, NT80_SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE"}, "clinvarAccession": {"accession": "SCV000020155", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-01-30T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": 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(2010) identified a homozygous complex insertion/deletion mutation in exon 2 of the KIAA0415 gene. The mutation comprised a 4-bp deletion (80del4) and a 22-bp insertion (84ins22), resulting in a frameshift and premature stop codon following residue 29. The insertion was found to be an imperfect quadruplication of a sequence, suggesting DNA polymerase slippage during DNA synthesis as the pathogenetic mechanism. The patients presented with progressive spastic paraplegia associated with urinary incontinence from ages 50 and 49 years, respectively. One had a normal cerebral MRI, whereas the other had spinal hyperintensities in the cervical spine. The unaffected parents were not known to be consanguineous, but they originated from 2 neighboring villages. The mutation was not found in 156 Caucasian or 242 North African control chromosomes. Studies of lymphoblastoid cells derived from 1 patient showed increased sensitivity to DNA-damaging drugs. The findings suggested a link between this form of spastic paraplegia, which could be considered a neurodegenerative disease, and defects in DNA repair."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20613862", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "613647", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "AP5Z1"}], "name": {"value": "AP5Z1, 4-BP DEL/22-BP INS, NT80"}, "variantType": "Variation", "otherNames": [{"value": "4-BP DEL/22-BP INS, NT80", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613653.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20155"}, {"clinvarSubmissionId": {"localKey": "NM_014855.3:c.80_83delinsTGCTGTAAACTGTAACTGTAAA|OMIM:613647", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001451119", "version": 1, "submitterIdentifiers": {"submitterName": "Paris 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"loss of function", "integerValue": "273"}, "type": "disease mechanism"}, "xrefs": [{"db": "Genetic Testing Registry (GTR)", "id": "GTR000561373"}]}, {"attribute": {"base": {"integerValue": "10738"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10738"}]}], "citations": [{"ids": [{"value": "26401545", "source": "PubMed"}, {"value": "NBK316514", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "416"}, {"db": "Orphanet", "id": "93600"}, {"db": "MedGen", "id": "C3150878"}, {"db": "MONDO", "id": "MONDO:0013327"}, {"db": "OMIM", "id": "613616", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "19", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2010-09-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": 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(1995) presented evidence for 2 different genetic backgrounds giving rise to the Fy(a-b-) phenotype. The most likely genetic mechanism in most individuals is downregulation of Duffy glycoprotein mRNA (see 613665.0002). However, the Duffy gene from a very rare Caucasian individual (AZ) with the Fy(a-b-) phenotype had a 14-bp deletion that resulted in a frameshift. In the Abstract and Results sections of their paper, Mallinson et al. (1995) reported that the deletion removed nucleotides 287 to 301 of DARC. However, their Figure 4 showed that the deletion involved nucleotides 292 to 305, which appeared to be correct. The DARC cDNA sequence used by Mallinson et al. (1995) was identical to that of the minor DARC variant reported by Chaudhuri et al. (1993). The frameshift resulting from the deletion introduced a stop codon 23 amino acids downstream and produced a putative truncated 118-amino acid protein. 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(1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. They found that in some of these cases Fy(b-) individuals had the wildtype FY*B GATA but carried 271C-T and 304G-A mutations. The 271C-T substitution resulted in an R91C amino acid substitution (R89C in the predominant DARC isoform reported by Iwamoto et al. (1996)), which represented a considerable change of chemical nature, one that may affect the antigenic determinants of DARC, and thus may be of clinical significance. Parasol et al. (1998) noted that further studies were needed to determine whether erythrocytes carrying these mutations behave as Fy(bwk) variants."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9746760", "source": "PubMed"}]}, {"ids": [{"value": "8547665", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Carrington et al. (1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. 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b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_custom_score.xml/out.jsonl index e4dfa74..dedfe94 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_custom_score.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_custom_score.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "1810274", "variationName": "NM_016023.5(OTUD6B):c.401A>G (p.Glu134Gly)", "variationType": "single nucleotide variant", "dateCreated": "2023-01-07T00:00:00Z", "dateLastUpdated": "2024-01-26T00:00:00Z", "mostRecentSubmission": "2024-01-26T00:00:00Z", "accession": "VCV001810274", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["8q21.3"], "sequenceLocations": [{"assembly": "GRCh38", "chr": 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"affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_ALLELES"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_016023.5:c.401A>G"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "617452"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB12515886"], "id": "5502945"}], "traitMappings": [{"medgens": [{"name": "Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies", "cui": "C4479520"}], "clinicalAssertionId": "5502945", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "617452", "mappingRef": "OMIM"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_flagged_submission.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_flagged_submission.xml/out.jsonl index ed8dafc..90d3c0f 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_flagged_submission.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_flagged_submission.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "9474", "variationName": "NM_001298.3(CNGA3):c.847C>T (p.Arg283Trp)", "variationType": "single nucleotide variant", "dateCreated": "2017-01-13T00:00:00Z", "dateLastUpdated": "2024-04-15T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "accession": "VCV000009474", "version": 32, "numberOfSubmitters": 9, "numberOfSubmissions": 11, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["2q11.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 98346456, "stop": 98398601, "displayStart": 98346456, 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{"nucleotideExpression": {"expression": "NG_009097.1:g.54863C>T", "sequenceAccessionVersion": "NG_009097.1", "sequenceAccession": "NG_009097", "sequenceVersion": 1, "change": "g.54863C>T"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001079878.2:c.793C>T", "sequenceAccessionVersion": "NM_001079878.2", "sequenceAccession": "NM_001079878", "sequenceVersion": 2, "change": "c.793C>T"}, "proteinExpression": {"expression": "NP_001073347.1:p.Arg265Trp", "sequenceAccessionVersion": "NP_001073347.1", "sequenceAccession": "NP_001073347", "sequenceVersion": 1, "change": "p.Arg265Trp"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_001298.3:c.847C>T", "sequenceAccessionVersion": "NM_001298.3", "sequenceAccession": "NM_001298", "sequenceVersion": 3, "change": "c.847C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_001289.1:p.Arg283Trp", 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Visual acuity is usually stable over time; both nystagmus and sensitivity to bright light may improve slightly. Although the fundus is usually normal, macular changes (which may show early signs of progression) and vessel narrowing may be present in some affected individuals. Defects in the macula are visible on optical coherence tomography."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1418"}]}, {"attribute": {"base": {"integerValue": "9649"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "9649"}]}], "citations": [{"ids": [{"value": "20301591", "source": "PubMed"}, {"value": "NBK1418", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "3110037", "source": "pmc"}], "type": "Translational/Evidence-based", "abbrev": "EuroGentest, 2011"}], "xrefs": [{"db": "Orphanet", "id": "49382"}, {"db": "MedGen", "id": "C1857618"}, {"db": "MONDO", "id": "MONDO:0009003"}, {"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "6436", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "Monochromacy", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0007803"}]}], "xrefs": [{"db": "MedGen", "id": "C5201048"}, {"db": "Human Phenotype Ontology", "id": "HP:0007803", "type": "primary"}, {"db": "Human Phenotype Ontology", "id": "HP:0007954", "type": "secondary"}]}], "type": "TYPE_FINDING", "id": "34298", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2024-01-23T00:00:00Z", "dateCreated": "2017-01-13T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "numberOfSubmitters": 9, "numberOfSubmissions": 11}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "600053.0002_ACHROMATOPSIA 2", "title": "CNGA3, ARG283TRP_ACHROMATOPSIA 2"}, "clinvarAccession": {"accession": "SCV000030303", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-04-21T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-10-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In affected members of a family with rod monochromacy (ACHM2; 216900), Kohl et al. (1998) found homozygosity for a C-to-T transition at nucleotide 887 of the CNGA3 gene, resulting in an arg283-to-trp (R283W) substitution."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9662398", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}, {"attributes": [{"base": {"value": "Wissinger et al. (2001) found the R283W mutation in 19 of 110 mutant alleles, including 14 alleles in 7 homozygous patients. Haplotype analysis suggested that these alleles, which were particularly frequent among patients from Scandinavia and northern Italy, have a common origin. Some of the patients homozygous for this mutation had complete achromatopsia with no detectable cone function, whereas others had incomplete achromatopsia with residual cone ERG responses and/or color vision."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "11536077", "source": "PubMed"}]}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "names": [{"value": "CNGA3, ARG283TRP"}], "variantType": "Variation", "otherNames": [{"value": "ARG283TRP", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "600053.0002", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "ACHROMATOPSIA 2", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "30303"}, {"clinvarSubmissionId": {"localKey": "GDXSV:216529", "localKeyIsSubmitted": false}, "clinvarAccession": {"accession": "SCV001773382", "version": 3, "submitterIdentifiers": {"submitterName": "GeneDx", "orgId": "26957", "orgCategory": "laboratory"}, "dateUpdated": "2023-03-04T00:00:00Z", "dateCreated": "2021-08-07T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "comments": [{"value": "Published functional studies demonstrate a damaging effect consistent with loss-of-function (Muraki-Oda et al., 2007; Ding et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26992781, 31237654, 32141364, 20238023, 24504161, 9662398, 16319819, 17693388, 11536077, 30682209, 31877759, 32869108, 33562422, 32037395)"}], "dateLastEvaluated": "2021-11-26T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "GeneDx Variant Classification Process June 2021"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/fc81e176/genedx_variant_classification_process_june_2021.pdf"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "otherNames": [{"value": "GDX:724380", "type": "SubmitterVariantId"}], "attributes": [{"attribute": {"base": {"value": "NM_001298.2:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "Not Provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["GeneDX_Clinvar_Submission_20_20210805063641", "GeneDX_Clinvar_Submission_74_20211208054205"], "id": "3482937"}, {"clinvarSubmissionId": {"localKey": "50189|OMIM:216900", "submittedAssembly": "GRCh38"}, "clinvarAccession": {"accession": "SCV004041266", "version": 1, "submitterIdentifiers": {"submitterName": "Baylor Genetics", "orgId": "1006", "orgCategory": "laboratory"}, "dateUpdated": "2023-10-07T00:00:00Z", "dateCreated": "2023-10-07T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2023-07-08T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_001298.3:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB13858663"], "id": "7562760"}, {"clinvarSubmissionId": {"localKey": "112028|MedGen:CN517202", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV002063881", "version": 14, "submitterIdentifiers": {"submitterName": "CeGaT Center for Human Genetics Tuebingen", "orgId": "505870", "orgCategory": "laboratory", "orgAbbreviation": "CHGT"}, "dateUpdated": "2024-04-15T00:00:00Z", "dateCreated": "2022-01-26T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2022-10-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/api/2.0/files/0ynenhfo/cegat_center_for_human_genetics_tuebingen_-_variant_classification_criteria_-_version_2.pdf/?format=attachment"}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "4"}, "type": "TYPE_VARIANT_ALLELES"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "stop": 99012480, "variantLength": 1, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"xrefs": [{"db": "MedGen", "id": "CN517202", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["2022-01", "2022-01-corrected", "2022-04", "2022-07", "2022-08", "2022-10.3", "2023-01", "2023-04", "2023-09-add-ACMG-details", "2023-10", "2024-04", "SUB13641132", "SUB13985080", "SUB14102099", "SUB14290090"], "id": "4044408"}, {"clinvarSubmissionId": {"localKey": "CMGVARID00576|HPO:HP:0007803", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV000492977", "version": 1, "submitterIdentifiers": {"submitterName": "Centre for Mendelian Genomics, University Medical Centre Ljubljana", "orgId": "505952", "orgCategory": "clinic", "orgAbbreviation": "CMG-UMCL"}, "dateUpdated": "2017-01-13T00:00:00Z", "dateCreated": "2017-01-13T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "dateLastEvaluated": "2014-07-21T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": 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and MUMC+", "orgId": "505925", "orgCategory": "laboratory", "orgAbbreviation": "Radboudumc_MUMC+"}, "dateUpdated": "2018-09-10T00:00:00Z", "dateCreated": "2018-09-10T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2016-09-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_ALLELES"}]}, {"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_CHROMOSOMES"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_001298.2:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "studyDescription": "Variants as described in Haer-Wigman et al. 2016", "submissionNames": ["haerwigman2016"], "id": "1569297"}, {"clinvarSubmissionId": {"localKey": "NM_001298.2:c.847C>T|OMIM:216900", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001367338", "version": 2, "submitterIdentifiers": {"submitterName": "Centre for Mendelian Genomics, University Medical Centre Ljubljana", "orgId": "505952", "orgCategory": "clinic", "orgAbbreviation": "CMG-UMCL"}, "dateUpdated": "2020-12-12T00:00:00Z", "dateCreated": "2020-07-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PM1,PM2,PM5,PP3,PP5."}], "dateLastEvaluated": "2019-09-12T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_001298.2:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB8622351"], "id": "2695419"}, {"clinvarSubmissionId": {"localKey": "report_configuration_variant_id:3272964"}, "clinvarAccession": {"accession": "SCV001905566", "version": 1, "submitterIdentifiers": {"submitterName": "Institute of Medical Genetics and Applied Genomics, University Hospital T\u00fcbingen", "orgId": "506385", "orgCategory": "laboratory", "orgAbbreviation": "IMGAG"}, "dateUpdated": "2021-09-25T00:00:00Z", "dateCreated": "2021-09-25T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2021-09-15T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Autosomal recessive inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}, {"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_MALE"}, "observedData": [{"attributes": [{"base": {"value": "DX2106067"}, "type": "TYPE_SAMPLE_LOCAL_ID"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0011516"}]}], "type": "TYPE_FINDING"}}], "simpleAllele": {"variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "3745783"}, {"clinvarSubmissionId": {"localKey": ":Chr.2_99012480_99012480_C_T|not provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001956988", "version": 1, "submitterIdentifiers": {"submitterName": "Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+", "orgId": "505925", "orgCategory": "laboratory", "orgAbbreviation": "Radboudumc_MUMC+"}, "dateUpdated": "2021-10-02T00:00:00Z", "dateCreated": "2021-10-02T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen", "orgId": "506382", "orgCategory": "laboratory"}, "type": "TYPE_BEHALF"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "stop": 99012480, "variantLength": 1, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "studyName": "VKGL Data-share Consensus", "submissionNames": ["SUB10449206"], "id": "3838167"}, {"clinvarSubmissionId": {"localKey": ":Chr.2_99012480_99012480_C_T|not provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001966736", "version": 1, "submitterIdentifiers": {"submitterName": "Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center", "orgId": "506497", "orgCategory": "laboratory", "orgAbbreviation": "CGDx-EMC"}, "dateUpdated": "2021-10-07T00:00:00Z", "dateCreated": "2021-10-07T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen", "orgId": "506382", "orgCategory": "laboratory"}, "type": "TYPE_BEHALF"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "stop": 99012480, "variantLength": 1, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "studyName": "VKGL Data-share Consensus", "submissionNames": ["SUB10405229"], "id": "3859083"}, {"clinvarSubmissionId": {"localKey": "2474236|MedGen:CN517202", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001394271", "version": 5, "submitterIdentifiers": {"submitterName": "Invitae", "orgId": "500031", "orgCategory": "laboratory", "orgAbbreviation": "Invitae"}, "dateUpdated": "2024-02-14T00:00:00Z", "dateCreated": "2020-07-16T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "citations": [{"ids": [{"value": "9662398", "source": "PubMed"}]}, {"ids": [{"value": "11536077", "source": "PubMed"}]}, {"ids": [{"value": "24504161", "source": "PubMed"}]}, {"ids": [{"value": "25637600", "source": "PubMed"}]}, {"ids": [{"value": "26992781", "source": "PubMed"}]}, {"ids": [{"value": "17693388", "source": "PubMed"}]}, {"ids": [{"value": "20238023", "source": "PubMed"}]}], "comments": [{"value": "This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 283 of the CNGA3 protein (p.Arg283Trp). This variant is present in population databases (rs104893613, gnomAD 0.02%). This missense change has been observed in individual(s) with achromatopsia (PMID: 9662398, 11536077, 24504161, 25637600, 26992781). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9474). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CNGA3 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects CNGA3 function (PMID: 17693388, 20238023). For these reasons, this variant has been classified as Pathogenic."}], "dateLastEvaluated": "2024-01-23T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Invitae Variant Classification Sherloc (09022015)"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "28492532", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NC_000002.11:g.99012480C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MedGen", "id": "CN517202", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB11431369", "SUB12507860", "SUB14200283", "SUB8755776"], "id": "2729182"}], "traitMappings": [{"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3745783", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "4044408", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Monochromacy", "cui": "C5201048"}], "clinicalAssertionId": "962633", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0007803", "mappingRef": "HP"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "2729182", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "1569297", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia", "cui": "C0152200"}], "clinicalAssertionId": "3745783", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0011516", "mappingRef": "HP"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3482937", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Not Provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3859083", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3838167", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "2695419", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "7562760", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "30303", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "ACHROMATOPSIA 2", "mappingRef": "Preferred"}]}} +{"variationId": "9474", "variationName": "NM_001298.3(CNGA3):c.847C>T (p.Arg283Trp)", "variationType": "single nucleotide variant", "dateCreated": "2017-01-13T00:00:00Z", "dateLastUpdated": "2024-04-15T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "accession": "VCV000009474", "version": 32, "numberOfSubmitters": 9, "numberOfSubmissions": 11, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["2q11.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 98346456, "stop": 98398601, "displayStart": 98346456, "displayStop": 98398601, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 98962617, "stop": 99015063, "displayStart": 98962617, "displayStop": 99015063, "strand": "+"}]}], "omims": ["600053"], "fullName": "cyclic nucleotide gated channel subunit alpha 3", "geneId": "1261", "hgncId": "HGNC:2150", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_001298.3(CNGA3):c.847C>T (p.Arg283Trp)", "canonicalSpdi": "NC_000002.12:98396016:C:T", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["2q11.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": 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'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."}, "type": "public definition"}}], "xrefs": [{"db": "MedGen", "id": "C3661900"}]}], "type": "TYPE_DISEASE", "id": "9460", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "Colorblindness, total", "type": "Alternate"}, {"value": "Rod monochromatism 2", "type": "Alternate"}, {"value": "Rod monochromacy 2", "type": "Alternate"}, {"value": "Achromatopsia 2", "type": "Preferred", "xrefs": [{"db": "Genetic Alliance", "id": "Achromatopsia+2/116"}, {"db": "MONDO", "id": "MONDO:0009003"}]}], "symbols": [{"value": "ACHM2", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}, {"value": "RMCH2", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}, {"value": "CNGA3", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"value": "Achromatopsia is characterized by reduced visual acuity, pendular nystagmus, increased sensitivity to light (photophobia), a small central scotoma, eccentric fixation, and reduced or complete loss of color discrimination. 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Visual acuity is usually stable over time; both nystagmus and sensitivity to bright light may improve slightly. Although the fundus is usually normal, macular changes (which may show early signs of progression) and vessel narrowing may be present in some affected individuals. Defects in the macula are visible on optical coherence tomography."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1418"}]}, {"attribute": {"base": {"integerValue": "9649"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "9649"}]}], "citations": [{"ids": [{"value": "20301591", "source": "PubMed"}, {"value": "NBK1418", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "3110037", "source": "pmc"}], "type": "Translational/Evidence-based", "abbrev": "EuroGentest, 2011"}], "xrefs": [{"db": "Orphanet", "id": "49382"}, {"db": "MedGen", "id": "C1857618"}, {"db": "MONDO", "id": "MONDO:0009003"}, {"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "6436", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "Monochromacy", "type": "Preferred", "xrefs": [{"db": "Human Phenotype Ontology", "id": "HP:0007803"}]}], "xrefs": [{"db": "MedGen", "id": "C5201048"}, {"db": "Human Phenotype Ontology", "id": "HP:0007803", "type": "primary"}, {"db": "Human Phenotype Ontology", "id": "HP:0007954", "type": "secondary"}]}], "type": "TYPE_FINDING", "id": "34298", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2024-01-23T00:00:00Z", "dateCreated": "2017-01-13T00:00:00Z", "mostRecentSubmission": "2024-04-15T00:00:00Z", "numberOfSubmitters": 9, "numberOfSubmissions": 11}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "600053.0002_ACHROMATOPSIA 2", "title": "CNGA3, ARG283TRP_ACHROMATOPSIA 2"}, "clinvarAccession": {"accession": "SCV000030303", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-04-21T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-10-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In affected members of a family with rod monochromacy (ACHM2; 216900), Kohl et al. 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Some of the patients homozygous for this mutation had complete achromatopsia with no detectable cone function, whereas others had incomplete achromatopsia with residual cone ERG responses and/or color vision."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "11536077", "source": "PubMed"}]}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "name": {"value": "CNGA3, ARG283TRP"}, "variantType": "Variation", "otherNames": [{"value": "ARG283TRP", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "600053.0002", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "ACHROMATOPSIA 2", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "30303"}, {"clinvarSubmissionId": {"localKey": "GDXSV:216529", "localKeyIsSubmitted": false}, "clinvarAccession": {"accession": "SCV001773382", "version": 3, "submitterIdentifiers": {"submitterName": "GeneDx", "orgId": "26957", "orgCategory": "laboratory"}, "dateUpdated": "2023-03-04T00:00:00Z", "dateCreated": 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"orgCategory": "laboratory", "orgAbbreviation": "Radboudumc_MUMC+"}, "dateUpdated": "2018-09-10T00:00:00Z", "dateCreated": "2018-09-10T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2016-09-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_ALLELES"}]}, {"attributes": [{"base": {"integerValue": "1"}, "type": "TYPE_VARIANT_CHROMOSOMES"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_001298.2:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "studyDescription": "Variants as described in Haer-Wigman et al. 2016", "submissionNames": ["haerwigman2016"], "id": "1569297"}, {"clinvarSubmissionId": {"localKey": "NM_001298.2:c.847C>T|OMIM:216900", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001367338", "version": 2, "submitterIdentifiers": {"submitterName": "Centre for Mendelian Genomics, University Medical Centre Ljubljana", "orgId": "505952", "orgCategory": "clinic", "orgAbbreviation": "CMG-UMCL"}, "dateUpdated": "2020-12-12T00:00:00Z", "dateCreated": "2020-07-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely pathogenic", "comments": [{"value": "This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PM1,PM2,PM5,PP3,PP5."}], "dateLastEvaluated": "2019-09-12T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_001298.2:c.847C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "216900", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB8622351"], "id": "2695419"}, {"clinvarSubmissionId": {"localKey": "report_configuration_variant_id:3272964"}, "clinvarAccession": {"accession": "SCV001905566", "version": 1, "submitterIdentifiers": {"submitterName": "Institute of Medical Genetics and Applied Genomics, University Hospital T\u00fcbingen", "orgId": "506385", "orgCategory": "laboratory", "orgAbbreviation": "IMGAG"}, "dateUpdated": "2021-09-25T00:00:00Z", "dateCreated": "2021-09-25T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2021-09-15T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Autosomal recessive inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}, {"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_MALE"}, "observedData": [{"attributes": [{"base": {"value": "DX2106067"}, "type": "TYPE_SAMPLE_LOCAL_ID"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0011516"}]}], "type": "TYPE_FINDING"}}], "simpleAllele": {"variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "3745783"}, {"clinvarSubmissionId": {"localKey": ":Chr.2_99012480_99012480_C_T|not provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001956988", "version": 1, "submitterIdentifiers": {"submitterName": "Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+", "orgId": "505925", "orgCategory": "laboratory", "orgAbbreviation": "Radboudumc_MUMC+"}, "dateUpdated": "2021-10-02T00:00:00Z", "dateCreated": "2021-10-02T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen", "orgId": "506382", "orgCategory": "laboratory"}, "type": "TYPE_BEHALF"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "stop": 99012480, "variantLength": 1, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "studyName": "VKGL Data-share Consensus", "submissionNames": ["SUB10449206"], "id": "3838167"}, {"clinvarSubmissionId": {"localKey": ":Chr.2_99012480_99012480_C_T|not provided", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001966736", "version": 1, "submitterIdentifiers": {"submitterName": "Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center", "orgId": "506497", "orgCategory": "laboratory", "orgAbbreviation": "CGDx-EMC"}, "dateUpdated": "2021-10-07T00:00:00Z", "dateCreated": "2021-10-07T00:00:00Z"}, "additionalSubmitters": [{"submitterIdentifiers": {"submitterName": "Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen", "orgId": "506382", "orgCategory": "laboratory"}, "type": "TYPE_BEHALF"}], "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "start": 99012480, "stop": 99012480, "variantLength": 1, "referenceAllele": "C", "alternateAllele": "T"}]}}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "studyName": "VKGL Data-share Consensus", "submissionNames": ["SUB10405229"], "id": "3859083"}, {"clinvarSubmissionId": {"localKey": "2474236|MedGen:CN517202", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001394271", "version": 5, "submitterIdentifiers": {"submitterName": "Invitae", "orgId": "500031", "orgCategory": "laboratory", "orgAbbreviation": "Invitae"}, "dateUpdated": "2024-02-14T00:00:00Z", "dateCreated": "2020-07-16T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "citations": [{"ids": [{"value": "9662398", "source": "PubMed"}]}, {"ids": [{"value": "11536077", "source": "PubMed"}]}, {"ids": [{"value": "24504161", "source": "PubMed"}]}, {"ids": [{"value": "25637600", "source": "PubMed"}]}, {"ids": [{"value": "26992781", "source": "PubMed"}]}, {"ids": [{"value": "17693388", "source": "PubMed"}]}, {"ids": [{"value": "20238023", "source": "PubMed"}]}], "comments": [{"value": "This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 283 of the CNGA3 protein (p.Arg283Trp). This variant is present in population databases (rs104893613, gnomAD 0.02%). This missense change has been observed in individual(s) with achromatopsia (PMID: 9662398, 11536077, 24504161, 25637600, 26992781). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9474). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CNGA3 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects CNGA3 function (PMID: 17693388, 20238023). For these reasons, this variant has been classified as Pathogenic."}], "dateLastEvaluated": "2024-01-23T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Invitae Variant Classification Sherloc (09022015)"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "28492532", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "CNGA3"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NC_000002.11:g.99012480C>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MedGen", "id": "CN517202", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB11431369", "SUB12507860", "SUB14200283", "SUB8755776"], "id": "2729182"}], "traitMappings": [{"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3745783", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "4044408", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Monochromacy", "cui": "C5201048"}], "clinicalAssertionId": "962633", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0007803", "mappingRef": "HP"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "2729182", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "CN517202", "mappingRef": "MedGen"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "1569297", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia", "cui": "C0152200"}], "clinicalAssertionId": "3745783", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0011516", "mappingRef": "HP"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3482937", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Not Provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3859083", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "C3661900"}], "clinicalAssertionId": "3838167", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "2695419", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "7562760", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "216900", "mappingRef": "OMIM"}, {"medgens": [{"name": "Achromatopsia 2", "cui": "C1857618"}], "clinicalAssertionId": "30303", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "ACHROMATOPSIA 2", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_indication.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_indication.xml/out.jsonl index 4c6f8fb..367a842 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_indication.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_indication.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "226036", "variationName": "NM_003783.3(B3GALT2):c.367T>G (p.Tyr123Asp)", "variationType": "single nucleotide variant", "dateCreated": "2016-05-21T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": "2016-05-21T00:00:00Z", "accession": "VCV000226036", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["1q31.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 193178730, "stop": 193186613, "displayStart": 193178730, "displayStop": 193186613, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 193147859, "stop": 193155742, "displayStart": 193147859, "displayStop": 193155742, "strand": "-"}]}], "omims": ["603018"], "fullName": "beta-1,3-galactosyltransferase 2", "geneId": "8707", "hgncId": "HGNC:917", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_MULTIPLE_GENES_BY_OVERLAP"}, {"locations": [{"cytogeneticLocations": ["1q31.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 193122031, "stop": 193254815, "displayStart": 193122031, "displayStop": 193254815, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 193091087, "stop": 193223944, "displayStart": 193091087, "displayStop": 193223944, "strand": "+"}]}], "omims": ["607393"], "haploinsufficiency": {"value": "Sufficient evidence for dosage pathogenicity", "lastEvaluated": "2022-04-13T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=CDC73"}, "triplosensitivity": {"value": "No evidence available", "lastEvaluated": "2022-04-13T00:00:00Z", "clingen": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=CDC73"}, "fullName": "cell division cycle 73", "geneId": "79577", "hgncId": "HGNC:16783", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_MULTIPLE_GENES_BY_OVERLAP"}], "name": "NM_003783.3(B3GALT2):c.367T>G (p.Tyr123Asp)", "canonicalSpdi": "NC_000001.11:193181195:A:C", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["1q31.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 193181196, "stop": 193181196, "displayStart": 193181196, "displayStop": 193181196, "variantLength": 1, "positionVcf": 193181196, "referenceAlleleVcf": "A", "alternateAlleleVcf": "C"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 193150326, "stop": 193150326, "displayStart": 193150326, "displayStop": 193150326, "variantLength": 1, "positionVcf": 193150326, "referenceAlleleVcf": "A", "alternateAlleleVcf": "C"}]}], "proteinChanges": ["Y123D"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NC_000001.10:g.193150326A>C", "sequenceAccessionVersion": "NC_000001.10", "sequenceAccession": "NC_000001", "sequenceVersion": 10, "change": "g.193150326A>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000001.11:g.193181196A>C", "sequenceAccessionVersion": "NC_000001.11", "sequenceAccession": "NC_000001", "sequenceVersion": 11, "change": "g.193181196A>C"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_012691.1:g.64239A>C", "sequenceAccessionVersion": "NG_012691.1", "sequenceAccession": "NG_012691", "sequenceVersion": 1, "change": "g.64239A>C"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NG_052990.1:g.10418T>G", "sequenceAccessionVersion": "NG_052990.1", "sequenceAccession": "NG_052990", "sequenceVersion": 1, "change": "g.10418T>G"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_003783.3:c.367T>G", "sequenceAccessionVersion": "NM_003783.3", "sequenceAccession": "NM_003783", "sequenceVersion": 3, "change": "c.367T>G", "maneSelect": true}, "proteinExpression": {"expression": "NP_003774.1:p.Tyr123Asp", "sequenceAccessionVersion": "NP_003774.1", "sequenceAccession": "NP_003774", "sequenceVersion": 1, "change": "p.Tyr123Asp"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_024529.5:c.973-22599A>C", "sequenceAccessionVersion": "NM_024529.5", "sequenceAccession": "NM_024529", "sequenceVersion": 5, "change": "c.973-22599A>C", "maneSelect": true}, "molecularConsequences": [{"db": "SO", "id": "SO:0001627", "type": "intron variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "LRG_507:g.64239A>C", "sequenceAccessionVersion": "LRG_507", "sequenceAccession": "LRG_507"}, "type": "HGVS_TYPE_GENOMIC"}], "xrefs": [{"db": "ClinGen", "id": "CA1303641"}, {"db": "dbSNP", "id": "41265203", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.0006, "source": "1000 Genomes Project", "minorAllele": "C"}, "alleleId": "227841", "variationId": "226036"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Hyperparathyroidism 2 with jaw tumors", "db": "MedGen", "id": "C1704981"}], "traitSetId": "833"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely benign", "dateLastEvaluated": "2015-03-11T00:00:00Z", "submissionCount": 1}}}, "title": "NM_003783.3(B3GALT2):c.367T>G (p.Tyr123Asp) AND Hyperparathyroidism 2 with jaw tumors", "accession": "RCV000211442", "version": 2}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely benign", "conditions": [{"traits": [{"names": [{"value": "Hyperparathyroidism 2 with jaw tumors", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0007768"}]}, {"value": "HYPERPARATHYROIDISM, FAMILIAL PRIMARY, WITH MULTIPLE OSSIFYING JAW FIBROMAS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "HYPERPARATHYROIDISM-JAW TUMOR SYNDROME, HEREDITARY", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "Hyperparathyroidism 2", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Hyperparathyroidism+2/8598"}]}], "symbols": [{"value": "HPT-JT", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "HRPT2", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "CDC73-Related Disorders"}, "type": "keyword"}, "xrefs": [{"db": "GeneReviews", "id": "226120"}]}, {"attribute": {"base": {"value": "The spectrum of CDC73-related disorders includes the following phenotypes: Hyperparathyroidism-jaw tumor (HPT-JT) syndrome. Primary hyperparathyroidism, the main finding of HPT-JT syndrome, occurs in up to 95% of affected individuals; onset is typically in late adolescence or early adulthood. HPT-JT-associated primary hyperparathyroidism is usually caused by a single parathyroid adenoma. In approximately 10%-15% of individuals, primary hyperparathyroidism is caused by parathyroid carcinoma. Ossifying fibromas of the mandible or maxilla, also known as cementifying fibromas and cemento-ossifying fibromas, occur in 30%-40% of individuals with HPT-JT syndrome. Although benign, these tumors can be locally aggressive and may continue to enlarge if not treated. Approximately 20% of individuals with HPT-JT syndrome have kidney lesions, most commonly cysts; renal hamartomas and (more rarely) Wilms tumor have also been reported. Benign and malignant uterine tumors appear to be common in women with HPT-JT syndrome. Parathyroid carcinoma. Most parathyroid carcinomas are functional, resulting in hyperparathyroidism and a high serum calcium level; however, nonfunctioning parathyroid carcinomas are also rarely described in individuals with a CDC73-related disorder. A germline CDC73 pathogenic variant has been identified in 20%-29% of individuals with apparently sporadic parathyroid carcinoma. Familial isolated hyperparathyroidism (FIHP). FIHP is characterized by primary hyperparathyroidism without other associated syndromic features. Individuals with CDC73-related FIHP tend to have a more severe clinical presentation and younger age of onset than individuals with FIHP in whom a CDC73 pathogenic variant has not been identified."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK3789"}]}, {"attribute": {"base": {"integerValue": "10829"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10829"}]}], "citations": [{"ids": [{"value": "20301471", "source": "PubMed"}, {"value": "NBK1294", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "20301744", "source": "PubMed"}, {"value": "NBK3789", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "99880"}, {"db": "MedGen", "id": "C1704981"}, {"db": "MONDO", "id": "MONDO:0007768"}, {"db": "OMIM", "id": "145001", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "833", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2015-03-11T00:00:00Z", "dateCreated": "2016-05-21T00:00:00Z", "mostRecentSubmission": "2016-05-21T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "UWMG_6788739|MedGen:C1704981", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV000212171", "version": 1, "submitterIdentifiers": {"submitterName": "CSER _CC_NCGL, University of Washington", "orgId": "505295", "orgCategory": "laboratory", "orgAbbreviation": "CSER _CC_NCGL"}, "dateUpdated": "2016-05-21T00:00:00Z", "dateCreated": "2016-05-21T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely benign", "dateLastEvaluated": "2015-03-11T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Autosomal dominant inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}, {"attribute": {"value": "Amendola et al. 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[{"classifiedConditionList": {"classifiedConditions": [{"value": "Hyperparathyroidism 2 with jaw tumors", "db": "MedGen", "id": "C1704981"}], "traitSetId": "833"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Likely benign", "dateLastEvaluated": "2015-03-11T00:00:00Z", "submissionCount": 1}}}, "title": "NM_003783.3(B3GALT2):c.367T>G (p.Tyr123Asp) AND Hyperparathyroidism 2 with jaw tumors", "accession": "RCV000211442", "version": 2}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Likely benign", "conditions": [{"traits": [{"names": [{"value": "Hyperparathyroidism 2 with jaw tumors", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0007768"}]}, {"value": "HYPERPARATHYROIDISM, FAMILIAL PRIMARY, WITH MULTIPLE OSSIFYING JAW FIBROMAS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "HYPERPARATHYROIDISM-JAW TUMOR SYNDROME, HEREDITARY", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "Hyperparathyroidism 2", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Hyperparathyroidism+2/8598"}]}], "symbols": [{"value": "HPT-JT", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}, {"value": "HRPT2", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "145001", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "CDC73-Related Disorders"}, "type": "keyword"}, "xrefs": [{"db": "GeneReviews", "id": "226120"}]}, {"attribute": {"base": {"value": "The spectrum of CDC73-related disorders includes the following phenotypes: Hyperparathyroidism-jaw tumor (HPT-JT) syndrome. Primary hyperparathyroidism, the main finding of HPT-JT syndrome, occurs in up to 95% of affected individuals; onset is typically in late adolescence or early adulthood. HPT-JT-associated primary hyperparathyroidism is usually caused by a single parathyroid adenoma. In approximately 10%-15% of individuals, primary hyperparathyroidism is caused by parathyroid carcinoma. Ossifying fibromas of the mandible or maxilla, also known as cementifying fibromas and cemento-ossifying fibromas, occur in 30%-40% of individuals with HPT-JT syndrome. Although benign, these tumors can be locally aggressive and may continue to enlarge if not treated. Approximately 20% of individuals with HPT-JT syndrome have kidney lesions, most commonly cysts; renal hamartomas and (more rarely) Wilms tumor have also been reported. Benign and malignant uterine tumors appear to be common in women with HPT-JT syndrome. Parathyroid carcinoma. Most parathyroid carcinomas are functional, resulting in hyperparathyroidism and a high serum calcium level; however, nonfunctioning parathyroid carcinomas are also rarely described in individuals with a CDC73-related disorder. A germline CDC73 pathogenic variant has been identified in 20%-29% of individuals with apparently sporadic parathyroid carcinoma. Familial isolated hyperparathyroidism (FIHP). FIHP is characterized by primary hyperparathyroidism without other associated syndromic features. Individuals with CDC73-related FIHP tend to have a more severe clinical presentation and younger age of onset than individuals with FIHP in whom a CDC73 pathogenic variant has not been identified."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK3789"}]}, {"attribute": {"base": {"integerValue": "10829"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10829"}]}], "citations": [{"ids": [{"value": "20301471", "source": "PubMed"}, {"value": "NBK1294", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"value": "20301744", "source": "PubMed"}, {"value": "NBK3789", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "99880"}, {"db": "MedGen", "id": "C1704981"}, {"db": "MONDO", "id": "MONDO:0007768"}, {"db": "OMIM", "id": "145001", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "833", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2015-03-11T00:00:00Z", "dateCreated": "2016-05-21T00:00:00Z", "mostRecentSubmission": "2016-05-21T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "UWMG_6788739|MedGen:C1704981", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV000212171", "version": 1, "submitterIdentifiers": {"submitterName": "CSER _CC_NCGL, University of Washington", "orgId": "505295", "orgCategory": "laboratory", "orgAbbreviation": "CSER _CC_NCGL"}, "dateUpdated": "2016-05-21T00:00:00Z", "dateCreated": "2016-05-21T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Likely benign", "dateLastEvaluated": "2015-03-11T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "Autosomal dominant inheritance"}, "type": "TYPE_MODE_OF_INHERITANCE"}, {"attribute": {"value": "Amendola et al. (Genome Res. 2015)"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25637381", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN", "indication": {"traits": [{"names": [{"value": "adults with personal and/or family history of colorectal cancer and/or polyps", "type": "Preferred"}]}], "type": "TYPE_INDICATION"}}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"genes": [{"symbol": "B3GALT2"}, {"symbol": "CDC73"}], "variantType": "Variation", "otherNames": [{"value": "NM_003783.3:c.367T>G"}], "xrefs": [{"db": "dbSNP", "id": "41265203", "type": "rsNumber"}], "attributes": [{"attribute": {"base": {"value": "NC_000001.10:g.193150326A>C"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "Hyperparathyroidism-jaw tumor syndrome", "type": "Preferred"}], "xrefs": [{"db": "MedGen", "id": "C1704981", "type": "CUI"}]}], "type": "TYPE_DISEASE"}, "studyName": "CSER - NEXT Medicine variant annotation", "studyDescription": "Diagnostic and incidental finding variants identified by exome sequencing in participants having clinical genetic testing for hereditary colorectal cancer and/or polyps", "submissionNames": ["NEXT_V01_2"], "id": "504204"}], "traitMappings": [{"medgens": [{"name": "Hyperparathyroidism 2 with jaw tumors", "cui": "C1704981"}], "clinicalAssertionId": "504204", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Hyperparathyroidism-jaw tumor syndrome", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_missense.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_missense.xml/out.jsonl index 24ce662..268cc67 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_missense.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_missense.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "12205", "variationName": "NM_000490.5(AVP):c.143G>T (p.Gly48Val)", "variationType": "single nucleotide variant", "dateCreated": "2013-04-04T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "accession": "VCV000012205", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["20p13"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_20", "accession": "NC_000020.11", "start": 3082556, "stop": 3084724, "displayStart": 3082556, "displayStop": 3084724, "strand": "-"}, 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a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_no_unflagged.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_no_unflagged.xml/out.jsonl index fcd9ea7..51d6d13 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_no_unflagged.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_no_unflagged.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "127244", "variationName": "NM_014780.5(CUL7):c.2592T>G (p.Tyr864Ter)", "variationType": "single nucleotide variant", "dateCreated": "2014-05-09T00:00:00Z", "dateLastUpdated": "2024-04-06T00:00:00Z", "mostRecentSubmission": "2015-05-31T00:00:00Z", "accession": "VCV000127244", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": 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b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_replaces.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "29674", "variationName": "NM_000791.4(DHFR):c.458A>T (p.Asp153Val)", "variationType": "single nucleotide variant", "dateCreated": "2014-04-24T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2016-08-22T00:00:00Z", "accession": "VCV000029674", "version": 1, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["5q14.1"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_5", "accession": "NC_000005.10", "start": 80626226, "stop": 80654983, "displayStart": 80626226, "displayStop": 80654983, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_5", "accession": "NC_000005.9", "start": 79922044, "stop": 79950799, 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Treatment with folinic acid can ameliorate some of the symptoms."}, "type": "public definition"}, "xrefs": [{"db": "OMIM", "id": "613839", "type": "MIM"}]}], "xrefs": [{"db": "Orphanet", "id": "319651"}, {"db": "MedGen", "id": "C3151205"}, {"db": "MONDO", "id": "MONDO:0013456"}, {"db": "OMIM", "id": "613839", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "7481", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2011-02-11T00:00:00Z", "dateCreated": "2014-04-24T00:00:00Z", "mostRecentSubmission": "2016-08-22T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 2}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "126060.0002_MEGALOBLASTIC ANEMIA DUE TO DIHYDROFOLATE REDUCTASE DEFICIENCY", "title": "DHFR, ASP153VAL_MEGALOBLASTIC ANEMIA DUE TO DIHYDROFOLATE REDUCTASE DEFICIENCY"}, "clinvarAccession": {"accession": "SCV000043814", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2016-08-22T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2011-02-11T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 3 affected sibs, born of distantly related parents of European descent, with megaloblastic anemia due to dihydrofolate reductase deficiency (613839), Cario et al. 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Levels of 5-methyltetrahydrofolate (5-MTHF) in the CSF were low, but improved with folinic acid treatment."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "21310277", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "613839", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "DHFR"}], "name": {"value": "DHFR, ASP153VAL"}, "variantType": "Variation", "otherNames": [{"value": "ASP153VAL", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "126060.0002", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MEGALOBLASTIC ANEMIA DUE TO DIHYDROFOLATE REDUCTASE DEFICIENCY", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "49070"}, {"clinvarSubmissionId": {"localKey": "DHFR_001"}, "clinvarAccession": {"accession": "SCV000148827", "version": 1, "submitterIdentifiers": {"submitterName": "Clinic of Pediatric and Adolescent Medicine, University Hospital Ulm", "orgId": "504838", "orgCategory": "laboratory"}, "dateUpdated": "2014-04-24T00:00:00Z", "dateCreated": "2014-04-24T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "pathogenic", "comments": [{"value": "Converted during submission to Pathogenic.", "type": "COMMENT_TYPE_CONVERTED_BY_NCB"}]}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED", "numerTested": 1}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "otherNames": [{"value": "DHFR c.458A>T"}, {"value": "DHFR p.D153V"}, {"value": "DHFR p.Asp153Val"}], "citations": [{"ids": [{"value": "1060915", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "1099447", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "6700662", "source": "PubMed"}], "type": "general"}], "attributes": [{"attribute": {"base": {"value": "NM_000791.3:c.458A>T"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"names": [{"value": "not provided", "type": "Preferred"}], "xrefs": [{"db": "OMIM", "id": "126060", "type": "MIM", "status": "STATUS_UNDER_REVIEW"}]}], "type": "TYPE_DISEASE"}, "comments": [{"value": "dihydrofolate reductase (DHFR) deficiency. Causes macrocytic anemia and neurologic disease (atypical childhood absence epilepsy);variable phenotypic expression;treatment with follinic acid leads to normal blood counts and improvement of neurologic symptoms. Manuscript submitted for publication, therefore public release of this dbSNP submission only from the time of publication.", "type": "COMMENT_TYPE_PUBLIC"}, {"value": "Causes macrocytic anemia and neurologic disease (atypical childhood absence epilepsy);variable phenotypic expression; treatment with follinic acid leads to normal blood counts and improvement of neurologic symptoms.", "dataSource": "CuratedByNCBI", "type": "COMMENT_TYPE_PUBLIC"}], "submissionNames": ["DHFR_variant_HC01"], "id": "269026"}], "traitMappings": [{"medgens": [{"name": "Constitutional megaloblastic anemia with severe neurologic disease", "cui": "C3151205"}], "clinicalAssertionId": "49070", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "MEGALOBLASTIC ANEMIA DUE TO DIHYDROFOLATE REDUCTASE DEFICIENCY", "mappingRef": "Preferred"}, {"medgens": [{"name": "not provided", "cui": "CN517202"}], "clinicalAssertionId": "269026", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "not provided", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_review_status_ns.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_review_status_ns.xml/out.jsonl index 007b90f..5c05ee5 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_review_status_ns.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_review_status_ns.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "1708487", "variationName": "NM_001347721.2(DYRK1A):c.367G>T (p.Glu123Ter)", "variationType": "single nucleotide variant", "dateCreated": "2022-10-08T00:00:00Z", "dateLastUpdated": "2023-08-06T00:00:00Z", "mostRecentSubmission": "2022-10-08T00:00:00Z", "accession": "VCV001708487", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": 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"Alternate", "xrefs": [{"db": "OMIM", "id": "187950", "type": "MIM"}]}, {"value": "Thrombocythemia 1", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0008554"}]}], "symbols": [{"value": "THCYT1", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "187950", "type": "MIM"}]}], "xrefs": [{"db": "MedGen", "id": "C3277671"}, {"db": "MONDO", "id": "MONDO:0008554"}, {"db": "OMIM", "id": "187950", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "2608", "contributesToAggregateClassification": false}, {"traits": [{"names": [{"value": "Primary myelofibrosis", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0009692"}]}, {"value": "Myelofibrosis, somatic", "type": "Alternate"}, {"value": "Suspected idiopathic myelofibrosis", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"integerValue": "8618"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "8618"}]}, {"attribute": {"base": {"value": "Hereditary cancer syndrome"}, "type": 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{"db": "OMIM", "id": "187950", "type": "MIM"}]}, {"names": [{"value": "Primary myelofibrosis", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0009692"}]}, {"value": "Myelofibrosis, somatic", "type": "Alternate"}, {"value": "Suspected idiopathic myelofibrosis", "type": "Alternate"}], "attributes": [{"attribute": {"base": {"integerValue": "8618"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "8618"}]}, {"attribute": {"base": {"value": "Hereditary cancer syndrome"}, "type": "keyword"}}], "xrefs": [{"db": "Orphanet", "id": "824"}, {"db": "MedGen", "id": "C0001815"}, {"db": "MeSH", "id": "D055728"}, {"db": "MONDO", "id": "MONDO:0009692"}, {"db": "OMIM", "id": "254450", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "19309", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2022-02-10T00:00:00Z", "dateCreated": "2014-05-05T00:00:00Z", "mostRecentSubmission": "2022-12-31T00:00:00Z", "numberOfSubmitters": 2, "numberOfSubmissions": 3}, "somaticClinicalImpacts": [{"reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Tier I - Strong", "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "24325359", "source": "PubMed"}], "type": "general"}], "dateLastEvaluated": "2024-01-24T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z", "mostRecentSubmission": "2024-03-05T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 3}], "oncogenicityClassification": {"reviewStatus": "AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Uncertain significance", "citations": [{"ids": [{"value": "31562135", "source": "PubMed"}], "type": "general"}], "dateLastEvaluated": "2024-01-24T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z", "mostRecentSubmission": "2024-03-05T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "109091.0001_THROMBOCYTHEMIA, SOMATIC", "title": "CALR, 52-BP DEL, EX9_THROMBOCYTHEMIA, SOMATIC"}, "clinvarAccession": {"accession": "SCV000115336", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2014-05-05T00:00:00Z", "dateCreated": "2014-02-11T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2013-12-19T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_INCLUDED_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Klampfl et al. (2013) and Nangalia et al. (2013) identified a somatic 52-bp deletion in exon 9 of the CALR gene (1092_1143del) in patients with myeloproliferative neoplasms, including myelofibrosis (254450) and essential thrombocythemia (see 187950). CALR mutations and JAK2 and MPL mutations were mutually exclusive. The 52-bp mutation resulted in frameshift and premature termination (L367fsTer46). Klampfl et al. (2013) identified a total of 36 types of somatic insertion or deletion within exon 9 of CALR, all of which caused a frameshift to the same alternative reading frame and generated a novel C-terminal peptide in the mutant calreticulin. Klampfl et al. (2013) identified insertions or deletions in exon 9 of CALR in 88% of individuals with primary myelofibrosis with nonmutated JAK2 or MPL. The 52-bp deletion accounted for 53% of all cases of mutated CALR among several types of myeloproliferative neoplasm. Overexpression of this mutation resulted in cytokine-independent growth in vitro through the activation of STAT5 (601511). Nangalia et al. (2013) identified 23 patients with myelofibrosis who carried the L367fsTer46 mutation. Overall, Nangalia et al. (2013) identified 19 different somatic CALR mutations, all in exon 9 and all of which generated a +1 frameshift resulting in a mutant protein with a novel C terminal. CALR mutations were present in 18 of 32 patients (56%) with primary myelofibrosis and in 12 of 14 patients (86%) with progression of essential thrombocythemia to myelofibrosis. Neither Klampfl et al. (2013) nor Nangalia et al. (2013) detected CALR mutation in individuals with polycythemia vera."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}, {"ids": [{"value": "24325359", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}, {"db": "OMIM", "id": "187950", "type": "MIM"}, {"db": "OMIM", "id": "601511", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "names": [{"value": "CALR, 52-BP DEL, EX9"}], "variantType": "Variation", "otherNames": [{"value": "52-BP DEL, EX9", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "109091.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "THROMBOCYTHEMIA, SOMATIC", "type": "included"}]}], "type": "TYPE_DISEASE"}, "id": "202976"}, {"clinvarSubmissionId": {"localKey": "109091.0001_MYELOFIBROSIS, SOMATIC", "title": "CALR, 52-BP DEL, EX9_MYELOFIBROSIS, SOMATIC"}, "clinvarAccession": {"accession": "SCV000115335", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2014-05-05T00:00:00Z", "dateCreated": "2014-02-11T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2013-12-19T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Klampfl et al. (2013) and Nangalia et al. (2013) identified a somatic 52-bp deletion in exon 9 of the CALR gene (1092_1143del) in patients with myeloproliferative neoplasms, including myelofibrosis (254450) and essential thrombocythemia (see 187950). CALR mutations and JAK2 and MPL mutations were mutually exclusive. The 52-bp mutation resulted in frameshift and premature termination (L367fsTer46). Klampfl et al. (2013) identified a total of 36 types of somatic insertion or deletion within exon 9 of CALR, all of which caused a frameshift to the same alternative reading frame and generated a novel C-terminal peptide in the mutant calreticulin. Klampfl et al. (2013) identified insertions or deletions in exon 9 of CALR in 88% of individuals with primary myelofibrosis with nonmutated JAK2 or MPL. The 52-bp deletion accounted for 53% of all cases of mutated CALR among several types of myeloproliferative neoplasm. Overexpression of this mutation resulted in cytokine-independent growth in vitro through the activation of STAT5 (601511). Nangalia et al. (2013) identified 23 patients with myelofibrosis who carried the L367fsTer46 mutation. Overall, Nangalia et al. (2013) identified 19 different somatic CALR mutations, all in exon 9 and all of which generated a +1 frameshift resulting in a mutant protein with a novel C terminal. CALR mutations were present in 18 of 32 patients (56%) with primary myelofibrosis and in 12 of 14 patients (86%) with progression of essential thrombocythemia to myelofibrosis. Neither Klampfl et al. (2013) nor Nangalia et al. (2013) detected CALR mutation in individuals with polycythemia vera."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}, {"ids": [{"value": "24325359", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}, {"db": "OMIM", "id": "187950", "type": "MIM"}, {"db": "OMIM", "id": "601511", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "names": [{"value": "CALR, 52-BP DEL, EX9"}], "variantType": "Variation", "otherNames": [{"value": "52-BP DEL, EX9", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "109091.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MYELOFIBROSIS, SOMATIC", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "202975"}, {"clinvarSubmissionId": {"localKey": "NM_004343.4:c.1099_1150del|OMIM:187950;254450", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV002812646", "version": 1, "submitterIdentifiers": {"submitterName": "Fulgent Genetics, Fulgent Genetics", "orgId": "500105", "orgCategory": "laboratory"}, "dateUpdated": "2022-12-31T00:00:00Z", "dateCreated": "2022-12-31T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2022-02-10T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.4:c.1099_1150del"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "187950", "type": "MIM"}]}, {"xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}]}], "type": "TYPE_TRAIT_CHOICE"}, "submissionNames": ["SUB12390657"], "id": "5461412"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D015470|OncogenicityClassification", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697530", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - 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Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "somaticClinicalImpacts": {"value": "Tier I - Strong", "clinicalImpactAssertionType": "diagnostic", "clinicalImpactClinicalSignificance": "supports diagnosis"}, "citations": [{"ids": [{"value": "24325359", "source": "PubMed"}]}, {"ids": [{"value": "24325356", "source": "PubMed"}]}], "comments": [{"value": "A large majority of myeloproliferative neoplasms with nonmutated JAK2 exhibit somatic CALR mutations. In a subset of such cases with essential thrombocythemia, 67% had CALR mutation."}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with ET and 5-9% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "11%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, {"value": 79, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MAXIMUM"}], "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_FEMALE"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0031020"}]}], "type": "TYPE_FINDING", "dateLastEvaluated": "2021-04-15T00:00:00Z"}, "comments": [{"value": "A patient with a 10-year history of elevated and increasing platelet counts had a bone marrow biopsy in the absence of symptoms. The biopsy revealed thrombocythemia, with normal cytogenetics and without mutation of JAK2. CALR was not tested at that time. Approximately 2 \u00bd years later, a second BM biopsy was performed when the patient began having symptoms and counts were worsening. The biopsy had hypercellular marrow with 5-9% blasts and normal karyotype, but revealed this CALR exon 9 mutation at 11% allele frequency. She was started on 5-azyctadine; however, five months later, a BM biopsy showed 37% blasts positive for CD33, CD34, CD117, and HLA-DR, consistent with acute myeloid leukemia, and the karyotype included a novel translocation, t(4;7)(q12;q21.2), in 17 of 20 metaphase spreads examined. After induction chemotherapy with cytarabine and daunorubicin, a day-14 biopsy showed response to therapy, with a hypercellular marrow (80%) that displayed panmyelosis (trilineage hyperplasia), granulocytic hyperplasia, and megakaryocytic atypia without an increase in blasts, consistent with residual/persistent myeloid disease. A PB specimen revealed normocytic normochromatic anemia, leukocytosis, and thrombocytosis. Chromosome microarray analysis and NGS of DNA from a BM sample revealed no detectable genomic imbalances, the CALR deletion at 3.2% allele frequency, and no other pathogenic variants. After eight months in remission, the AML relapsed with blood DNA showing oncogenic somatic mutations at around 50% allele frequency, but no evidence of the CALR deletion."}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.3:c.1092_1143del52"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MeSH", "id": "D013920"}]}], "type": "TYPE_FINDING"}, "submissionNames": ["SUB14244255"], "id": "8771187"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D013920|ClinicalImpactClassification|prognostic", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697528", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "somaticClinicalImpacts": {"value": "Tier I - Strong", "clinicalImpactAssertionType": "prognostic", "clinicalImpactClinicalSignificance": "better outcome"}, "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}], "comments": [{"value": "In a cohort of 1107 myeloproliferative neoplasm patients, those with \"mutated CALR had a lower risk of thromobsis and longer overall survival than patients with mutated JAK2.\""}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with ET and 5-9% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "11%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, 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"type": "general"}], "dateLastEvaluated": "2024-01-24T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z", "mostRecentSubmission": "2024-03-05T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "109091.0001_THROMBOCYTHEMIA, SOMATIC", "title": "CALR, 52-BP DEL, EX9_THROMBOCYTHEMIA, SOMATIC"}, "clinvarAccession": {"accession": "SCV000115336", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2014-05-05T00:00:00Z", "dateCreated": "2014-02-11T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2013-12-19T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_INCLUDED_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Klampfl et al. (2013) and Nangalia et al. (2013) identified a somatic 52-bp deletion in exon 9 of the CALR gene (1092_1143del) in patients with myeloproliferative neoplasms, including myelofibrosis (254450) and essential thrombocythemia (see 187950). CALR mutations and JAK2 and MPL mutations were mutually exclusive. The 52-bp mutation resulted in frameshift and premature termination (L367fsTer46). Klampfl et al. (2013) identified a total of 36 types of somatic insertion or deletion within exon 9 of CALR, all of which caused a frameshift to the same alternative reading frame and generated a novel C-terminal peptide in the mutant calreticulin. Klampfl et al. (2013) identified insertions or deletions in exon 9 of CALR in 88% of individuals with primary myelofibrosis with nonmutated JAK2 or MPL. The 52-bp deletion accounted for 53% of all cases of mutated CALR among several types of myeloproliferative neoplasm. Overexpression of this mutation resulted in cytokine-independent growth in vitro through the activation of STAT5 (601511). Nangalia et al. (2013) identified 23 patients with myelofibrosis who carried the L367fsTer46 mutation. Overall, Nangalia et al. (2013) identified 19 different somatic CALR mutations, all in exon 9 and all of which generated a +1 frameshift resulting in a mutant protein with a novel C terminal. CALR mutations were present in 18 of 32 patients (56%) with primary myelofibrosis and in 12 of 14 patients (86%) with progression of essential thrombocythemia to myelofibrosis. Neither Klampfl et al. (2013) nor Nangalia et al. (2013) detected CALR mutation in individuals with polycythemia vera."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}, {"ids": [{"value": "24325359", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}, {"db": "OMIM", "id": "187950", "type": "MIM"}, {"db": "OMIM", "id": "601511", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "name": {"value": "CALR, 52-BP DEL, EX9"}, "variantType": "Variation", "otherNames": [{"value": "52-BP DEL, EX9", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "109091.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "THROMBOCYTHEMIA, SOMATIC", "type": "included"}]}], "type": "TYPE_DISEASE"}, "id": "202976"}, {"clinvarSubmissionId": {"localKey": "109091.0001_MYELOFIBROSIS, SOMATIC", "title": "CALR, 52-BP DEL, EX9_MYELOFIBROSIS, SOMATIC"}, "clinvarAccession": {"accession": "SCV000115335", "version": 2, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2014-05-05T00:00:00Z", "dateCreated": "2014-02-11T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2013-12-19T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Klampfl et al. (2013) and Nangalia et al. (2013) identified a somatic 52-bp deletion in exon 9 of the CALR gene (1092_1143del) in patients with myeloproliferative neoplasms, including myelofibrosis (254450) and essential thrombocythemia (see 187950). CALR mutations and JAK2 and MPL mutations were mutually exclusive. The 52-bp mutation resulted in frameshift and premature termination (L367fsTer46). Klampfl et al. (2013) identified a total of 36 types of somatic insertion or deletion within exon 9 of CALR, all of which caused a frameshift to the same alternative reading frame and generated a novel C-terminal peptide in the mutant calreticulin. Klampfl et al. (2013) identified insertions or deletions in exon 9 of CALR in 88% of individuals with primary myelofibrosis with nonmutated JAK2 or MPL. The 52-bp deletion accounted for 53% of all cases of mutated CALR among several types of myeloproliferative neoplasm. Overexpression of this mutation resulted in cytokine-independent growth in vitro through the activation of STAT5 (601511). Nangalia et al. (2013) identified 23 patients with myelofibrosis who carried the L367fsTer46 mutation. Overall, Nangalia et al. (2013) identified 19 different somatic CALR mutations, all in exon 9 and all of which generated a +1 frameshift resulting in a mutant protein with a novel C terminal. CALR mutations were present in 18 of 32 patients (56%) with primary myelofibrosis and in 12 of 14 patients (86%) with progression of essential thrombocythemia to myelofibrosis. Neither Klampfl et al. (2013) nor Nangalia et al. (2013) detected CALR mutation in individuals with polycythemia vera."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}, {"ids": [{"value": "24325359", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}, {"db": "OMIM", "id": "187950", "type": "MIM"}, {"db": "OMIM", "id": "601511", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "name": {"value": "CALR, 52-BP DEL, EX9"}, "variantType": "Variation", "otherNames": [{"value": "52-BP DEL, EX9", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "109091.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MYELOFIBROSIS, SOMATIC", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "202975"}, {"clinvarSubmissionId": {"localKey": "NM_004343.4:c.1099_1150del|OMIM:187950;254450", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV002812646", "version": 1, "submitterIdentifiers": {"submitterName": "Fulgent Genetics, Fulgent Genetics", "orgId": "500105", "orgCategory": "laboratory"}, "dateUpdated": "2022-12-31T00:00:00Z", "dateCreated": "2022-12-31T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2022-02-10T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_UNKNOWN"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.4:c.1099_1150del"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "187950", "type": "MIM"}]}, {"xrefs": [{"db": "OMIM", "id": "254450", "type": "MIM"}]}], "type": "TYPE_TRAIT_CHOICE"}, "submissionNames": ["SUB12390657"], "id": "5461412"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D015470|OncogenicityClassification", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697530", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "oncogenicityClassification": "Uncertain significance", "citations": [{"ids": [{"value": "31562135", "source": "PubMed"}]}], "comments": [{"value": "While there are strong associations of this variant to thrombocythemia and myeloproliferative neoplasms, its oncogenicity and clinical impact in this case of acute myeloid leukemia is uncertain because the allele frequency decreased over time from 11% (progressive thrombocythemia) to 3% (AML in remission) to undetectable at AML relapse."}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with 37% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "3%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, {"value": 79, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MAXIMUM"}], "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_FEMALE"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0031020"}]}, {"xrefs": [{"db": "HP", "id": "HP:0012138"}]}], "type": "TYPE_FINDING", "dateLastEvaluated": "2021-10-15T00:00:00Z"}}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.3:c.1092_1143del52"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MeSH", "id": "D015470"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB14244255"], "id": "8771190"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D013920|ClinicalImpactClassification|diagnostic", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697527", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "somaticClinicalImpact": {"value": "Tier I - Strong", "clinicalImpactAssertionType": "diagnostic", "clinicalImpactClinicalSignificance": "supports diagnosis"}, "citations": [{"ids": [{"value": "24325359", "source": "PubMed"}]}, {"ids": [{"value": "24325356", "source": "PubMed"}]}], "comments": [{"value": "A large majority of myeloproliferative neoplasms with nonmutated JAK2 exhibit somatic CALR mutations. In a subset of such cases with essential thrombocythemia, 67% had CALR mutation."}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with ET and 5-9% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "11%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, {"value": 79, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MAXIMUM"}], "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_FEMALE"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0031020"}]}], "type": "TYPE_FINDING", "dateLastEvaluated": "2021-04-15T00:00:00Z"}, "comments": [{"value": "A patient with a 10-year history of elevated and increasing platelet counts had a bone marrow biopsy in the absence of symptoms. The biopsy revealed thrombocythemia, with normal cytogenetics and without mutation of JAK2. CALR was not tested at that time. Approximately 2 \u00bd years later, a second BM biopsy was performed when the patient began having symptoms and counts were worsening. The biopsy had hypercellular marrow with 5-9% blasts and normal karyotype, but revealed this CALR exon 9 mutation at 11% allele frequency. She was started on 5-azyctadine; however, five months later, a BM biopsy showed 37% blasts positive for CD33, CD34, CD117, and HLA-DR, consistent with acute myeloid leukemia, and the karyotype included a novel translocation, t(4;7)(q12;q21.2), in 17 of 20 metaphase spreads examined. After induction chemotherapy with cytarabine and daunorubicin, a day-14 biopsy showed response to therapy, with a hypercellular marrow (80%) that displayed panmyelosis (trilineage hyperplasia), granulocytic hyperplasia, and megakaryocytic atypia without an increase in blasts, consistent with residual/persistent myeloid disease. A PB specimen revealed normocytic normochromatic anemia, leukocytosis, and thrombocytosis. Chromosome microarray analysis and NGS of DNA from a BM sample revealed no detectable genomic imbalances, the CALR deletion at 3.2% allele frequency, and no other pathogenic variants. After eight months in remission, the AML relapsed with blood DNA showing oncogenic somatic mutations at around 50% allele frequency, but no evidence of the CALR deletion."}]}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.3:c.1092_1143del52"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MeSH", "id": "D013920"}]}], "type": "TYPE_FINDING"}, "submissionNames": ["SUB14244255"], "id": "8771187"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D013920|ClinicalImpactClassification|prognostic", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697528", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "somaticClinicalImpact": {"value": "Tier I - Strong", "clinicalImpactAssertionType": "prognostic", "clinicalImpactClinicalSignificance": "better outcome"}, "citations": [{"ids": [{"value": "24325356", "source": "PubMed"}]}], "comments": [{"value": "In a cohort of 1107 myeloproliferative neoplasm patients, those with \"mutated CALR had a lower risk of thromobsis and longer overall survival than patients with mutated JAK2.\""}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with ET and 5-9% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "11%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, {"value": 79, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MAXIMUM"}], "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_FEMALE"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0031020"}]}], "type": "TYPE_FINDING", "dateLastEvaluated": "2021-04-15T00:00:00Z"}}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.3:c.1092_1143del52"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MeSH", "id": "D013920"}]}], "type": "TYPE_FINDING"}, "submissionNames": ["SUB14244255"], "id": "8771188"}, {"clinvarSubmissionId": {"localKey": "NM_004343.3:c.1092_1143del52|MeSH:D015470|ClinicalImpactClassification", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV004697529", "version": 1, "submitterIdentifiers": {"submitterName": "Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health", "orgId": "509422", "orgCategory": "laboratory"}, "dateUpdated": "2024-03-05T00:00:00Z", "dateCreated": "2024-03-05T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "somaticClinicalImpact": {"value": "Tier III - Unknown"}, "comments": [{"value": "While there are strong associations of this variant to thrombocythemia and myeloproliferative neoplasms, its oncogenicity and clinical impact in this case of acute myeloid leukemia is uncertain because the allele frequency decreased over time from 11% (progressive thrombocythemia) to 3% (AML in remission) to undetectable at AML relapse."}], "dateLastEvaluated": "2024-01-24T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_SOMATIC", "tissue": "bone marrow with 37% blasts", "somaticVariantInNormalTissue": "SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED", "somaticVariantAlleleFraction": "3%", "species": {"name": "human", "taxonomyId": 9606}, "ages": [{"value": 70, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MINIMUM"}, {"value": 79, "unit": "AGE_UNIT_YEARS", "type": "AGE_TYPE_MAXIMUM"}], "affectedStatus": "AFFECTED_STATUS_YES", "numerTested": 1, "gender": "GENDER_FEMALE"}, "observedData": [{"attributes": [{"base": {"value": "not provided"}, "type": "TYPE_DESCRIPTION"}]}], "traitSet": {"traits": [{"xrefs": [{"db": "HP", "id": "HP:0031020"}]}, {"xrefs": [{"db": "HP", "id": "HP:0012138"}]}], "type": "TYPE_FINDING", "dateLastEvaluated": "2021-10-15T00:00:00Z"}}], "simpleAllele": {"genes": [{"symbol": "CALR"}], "variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_004343.3:c.1092_1143del52"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "MeSH", "id": "D015470"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB14244255"], "id": "8771189"}], "traitMappings": [{"medgens": [{"name": "Acute myeloid leukemia", "cui": "C0023467"}], "clinicalAssertionId": "8771189", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "D015470", "mappingRef": "MeSH"}, {"medgens": [{"name": "Granulocytic hyperplasia", "cui": "C4023028"}], "clinicalAssertionId": "8771190", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0012138", "mappingRef": "HP"}, {"medgens": [{"name": "Thrombocythemia 1", "cui": "C3277671"}], "clinicalAssertionId": "5461412", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "187950", "mappingRef": "OMIM"}, {"medgens": [{"name": "Bone marrow hypercellularity", "cui": "C0427703"}], "clinicalAssertionId": "8771188", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0031020", "mappingRef": "HP"}, {"medgens": [{"name": "Primary myelofibrosis", "cui": "C0001815"}], "clinicalAssertionId": "5461412", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "254450", "mappingRef": "OMIM"}, {"medgens": [{"name": "Essential thrombocythemia", "cui": "C0040028"}], "clinicalAssertionId": "8771187", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "D013920", "mappingRef": "MeSH"}, {"medgens": [{"name": "Essential thrombocythemia", "cui": "C0040028"}], "clinicalAssertionId": "8771188", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "D013920", "mappingRef": "MeSH"}, {"medgens": [{"name": "Bone marrow hypercellularity", "cui": "C0427703"}], "clinicalAssertionId": "8771190", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0031020", "mappingRef": "HP"}, {"medgens": [{"name": "Bone marrow hypercellularity", "cui": "C0427703"}], "clinicalAssertionId": "8771187", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0031020", "mappingRef": "HP"}, {"medgens": [{"name": "Bone marrow hypercellularity", "cui": "C0427703"}], "clinicalAssertionId": "8771189", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0031020", "mappingRef": "HP"}, {"medgens": [{"name": "Thrombocythemia 1", "cui": "C3277671"}], "clinicalAssertionId": "202976", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "THROMBOCYTHEMIA, SOMATIC", "mappingRef": "Alternate"}, {"medgens": [{"name": "Acute myeloid leukemia", "cui": "C0023467"}], "clinicalAssertionId": "8771190", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "D015470", "mappingRef": "MeSH"}, {"medgens": [{"name": "Granulocytic hyperplasia", "cui": "C4023028"}], "clinicalAssertionId": "8771189", "traitType": "Finding", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "HP:0012138", "mappingRef": "HP"}, {"medgens": [{"name": "Primary myelofibrosis", "cui": "C0001815"}], "clinicalAssertionId": "202975", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "MYELOFIBROSIS, SOMATIC", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_study_description.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_study_description.xml/out.jsonl index 6598b89..e336dc5 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_study_description.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_study_description.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "34753", "variationName": "GRCh38/hg38 5p15.33(chr5:629340-820360)x1", "variationType": "copy number loss", "dateCreated": "2015-07-10T00:00:00Z", "dateLastUpdated": "2023-10-15T00:00:00Z", "mostRecentSubmission": "2015-07-10T00:00:00Z", "accession": "VCV000034753", "version": 2, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["5p15.33"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_5", "accession": "NC_000005.10", "start": 612340, "stop": 676616, "displayStart": 612340, "displayStop": 676616, "strand": "+"}, {"assembly": "GRCh38", "chr": "CHROMOSOME_5", "accession": "NT_187550.1", "start": 6636, "stop": 14557, "displayStart": 6636, "displayStop": 14557, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_5", "accession": "NC_000005.9", "start": 612404, "stop": 653667, "displayStart": 612404, "displayStop": 653667, "strand": "+"}]}], "omims": ["616475"], "fullName": "centrosomal protein 72", "geneId": "55722", "hgncId": "HGNC:25547", "source": "calculated", "relationshipType": "GENE_VARIANT_RELATIONSHIP_GENE_OVERLAPPED_BY_VARIANT"}, {"locations": [{"cytogeneticLocations": ["5p15.33"], "sequenceLocations": [{"assembly": 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AND/OR other significant developmental or morphological phenotypes", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_ethnicity.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_ethnicity.xml/out.jsonl index 20329aa..2290a60 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_ethnicity.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_ethnicity.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "654", "variationName": "NM_000130.5(F5):c.6304C>T (p.Arg2102Cys)", "variationType": "single nucleotide variant", "dateCreated": "2017-08-20T00:00:00Z", "dateLastUpdated": "2024-04-15T00:00:00Z", "mostRecentSubmission": "2019-09-29T00:00:00Z", "accession": "VCV000000654", "version": 3, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["1q24.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 169511951, "stop": 169586481, "displayStart": 169511951, "displayStop": 169586481, "strand": "-"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 169481191, "stop": 169555768, "displayStart": 169481191, "displayStop": 169555768, "strand": "-"}]}], "omims": ["612309"], "fullName": "coagulation factor V", "geneId": "2153", "hgncId": "HGNC:3542", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_000130.5(F5):c.6304C>T (p.Arg2102Cys)", "canonicalSpdi": "NC_000001.11:169518452:G:A", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["1q24.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 169518453, "stop": 169518453, "displayStart": 169518453, "displayStop": 169518453, "variantLength": 1, "positionVcf": 169518453, "referenceAlleleVcf": "G", "alternateAlleleVcf": "A"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 169487691, "stop": 169487691, "displayStart": 169487691, "displayStop": 169487691, "variantLength": 1, "positionVcf": 169487691, "referenceAlleleVcf": "G", "alternateAlleleVcf": "A"}]}], "otherNames": [{"value": "F5, ARG2074CYS"}, {"value": "R2074C"}], "proteinChanges": ["R2102C"], "hgvsExpressions": [{"proteinExpression": {"expression": "P12259:p.Arg2102Cys", "sequenceAccessionVersion": "P12259", "sequenceAccession": "P12259", "change": "p.Arg2102Cys"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "NC_000001.10:g.169487691G>A", "sequenceAccessionVersion": "NC_000001.10", "sequenceAccession": "NC_000001", 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Acquired thrombophilic disorders: antiphospholipid antibody (APLA) syndrome, paroxysmal nocturnal hemoglobinuria, myeloproliferative disorders, and increased levels of clotting factors. 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a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_hpo.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_hpo.xml/out.jsonl index 9667acb..981e730 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_hpo.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ex_with_hpo.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "7501", "variationName": "NM_002281.4(KRT81):c.1237G>A (p.Glu413Lys)", "variationType": "single nucleotide variant", "dateCreated": "2013-10-19T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2017-11-05T00:00:00Z", "accession": "VCV000007501", "version": 1, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": 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-{"variationId": "2", "variationName": "NM_014855.3(AP5Z1):c.80_83delinsTGCTGTAAACTGTAACTGTAAA (p.Arg27_Ile28delinsLeuLeuTer)", "variationType": "Indel", "dateCreated": "2017-01-30T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2021-05-16T00:00:00Z", "accession": "VCV000000002", "version": 3, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["7p22.1"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_7", "accession": "NC_000007.14", "start": 4775623, "stop": 4794397, "displayStart": 4775623, "displayStop": 4794397, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_7", "accession": "NC_000007.13", "start": 4815261, "stop": 4834025, "displayStart": 4815261, "displayStop": 4834025, "strand": "+"}]}], "omims": ["613653"], 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{"accession": "SCV000020155", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-01-30T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-06-29T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 French sibs with autosomal recessive spastic paraplegia-48 (SPG48; 613647), Slabicki et al. (2010) identified a homozygous complex insertion/deletion mutation in exon 2 of the KIAA0415 gene. The mutation comprised a 4-bp deletion (80del4) and a 22-bp insertion (84ins22), resulting in a frameshift and premature stop codon following residue 29. The insertion was found to be an imperfect quadruplication of a sequence, suggesting DNA polymerase slippage during DNA synthesis as the pathogenetic mechanism. The patients presented with progressive spastic paraplegia associated with urinary incontinence from ages 50 and 49 years, respectively. One had a normal cerebral MRI, whereas the other had spinal hyperintensities in the cervical spine. The unaffected parents were not known to be consanguineous, but they originated from 2 neighboring villages. The mutation was not found in 156 Caucasian or 242 North African control chromosomes. Studies of lymphoblastoid cells derived from 1 patient showed increased sensitivity to DNA-damaging drugs. The findings suggested a link between this form of spastic paraplegia, which could be considered a neurodegenerative disease, and defects in DNA repair."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20613862", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "613647", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "AP5Z1"}], "name": {"value": "AP5Z1, 4-BP DEL/22-BP INS, NT80"}, "variantType": "Variation", "otherNames": [{"value": "4-BP DEL/22-BP INS, NT80", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613653.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20155"}, {"clinvarSubmissionId": {"localKey": "NM_014855.3:c.80_83delinsTGCTGTAAACTGTAACTGTAAA|OMIM:613647", "submittedAssembly": "GRCh37"}, "clinvarAccession": {"accession": "SCV001451119", "version": 1, "submitterIdentifiers": {"submitterName": "Paris Brain Institute, Inserm - ICM", "orgId": "507826", "orgCategory": "laboratory"}, "dateUpdated": "2021-05-16T00:00:00Z", "dateCreated": "2021-05-16T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [{"attribute": {"value": "ACMG Guidelines, 2015"}, "type": "TYPE_ASSERTION_METHOD", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}]}]}], "observedIns": [{"sample": {"origin": "ORIGIN_UNKNOWN", "species": {"name": "human", "taxonomyId": 9606}, "affectedStatus": "AFFECTED_STATUS_YES"}, "observedData": [{"attributes": [{"base": {"integerValue": "2"}, "type": "TYPE_VARIANT_ALLELES"}]}]}], "simpleAllele": {"variantType": "Variation", "attributes": [{"attribute": {"base": {"value": "NM_014855.3:c.80_83delinsTGCTGTAAACTGTAACTGTAAA"}, "type": "HGVS"}}]}, "traitSet": {"traits": [{"xrefs": [{"db": "OMIM", "id": "613647", "type": "MIM"}]}], "type": "TYPE_DISEASE"}, "submissionNames": ["SUB8526155"], "id": "2865972"}], "traitMappings": [{"medgens": [{"name": "Hereditary spastic paraplegia 48", "cui": "C3150901"}], "clinicalAssertionId": "20155", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE", "mappingRef": "Preferred"}, {"medgens": [{"name": "Hereditary spastic paraplegia 48", "cui": "C3150901"}], "clinicalAssertionId": "2865972", "traitType": "Disease", "mappingType": "MAPPING_TYPE_XREF", "mappingValue": "613647", "mappingRef": "OMIM"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/one_record.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/one_record.xml/out.jsonl index c81393a..5a42f3a 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/one_record.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/one_record.xml/out.jsonl @@ -1 +1 @@ -{"variationId": "18396", "variationName": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)", "variationType": "single nucleotide variant", "dateCreated": "2017-12-15T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "accession": "VCV000018396", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["1q23.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 159204875, "stop": 159206500, "displayStart": 159204875, "displayStop": 159206500, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 159173802, "stop": 159176289, "displayStart": 159173802, "displayStop": 159176289, "strand": "+"}]}], "omims": ["613665"], "fullName": "atypical chemokine receptor 1 (Duffy blood group)", "geneId": "2532", "hgncId": "HGNC:4035", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)", "canonicalSpdi": "NC_000001.11:159205703:C:T", "variantTypes": ["single nucleotide variant"], "locations": [{"cytogeneticLocations": ["1q23.2"], "sequenceLocations": [{"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 159205704, "stop": 159205704, "displayStart": 159205704, "displayStop": 159205704, "variantLength": 1, "positionVcf": 159205704, "referenceAlleleVcf": "C", "alternateAlleleVcf": "T"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 159175494, "stop": 159175494, "displayStart": 159175494, "displayStop": 159175494, "variantLength": 1, "positionVcf": 159175494, "referenceAlleleVcf": "C", "alternateAlleleVcf": "T"}]}], "proteinChanges": ["R89C", "R91C"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NC_000001.10:g.159175494C>T", "sequenceAccessionVersion": "NC_000001.10", "sequenceAccession": "NC_000001", "sequenceVersion": 10, "change": "g.159175494C>T"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000001.11:g.159205704C>T", "sequenceAccessionVersion": "NC_000001.11", "sequenceAccession": "NC_000001", "sequenceVersion": 11, "change": "g.159205704C>T"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_011626.3:g.6692C>T", "sequenceAccessionVersion": "NG_011626.3", "sequenceAccession": "NG_011626", "sequenceVersion": 3, "change": "g.6692C>T"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001122951.3:c.271C>T", "sequenceAccessionVersion": "NM_001122951.3", "sequenceAccession": "NM_001122951", "sequenceVersion": 3, "change": "c.271C>T"}, "proteinExpression": {"expression": "NP_001116423.1:p.Arg91Cys", "sequenceAccessionVersion": "NP_001116423.1", "sequenceAccession": "NP_001116423", "sequenceVersion": 1, "change": "p.Arg91Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_002036.4:c.265C>T", "sequenceAccessionVersion": "NM_002036.4", "sequenceAccession": "NM_002036", "sequenceVersion": 4, "change": "c.265C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_002027.2:p.Arg89Cys", "sequenceAccessionVersion": "NP_002027.2", "sequenceAccession": "NP_002027", "sequenceVersion": 2, "change": "p.Arg89Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"proteinExpression": {"expression": "Q16570:p.Arg89Cys", "sequenceAccessionVersion": "Q16570", "sequenceAccession": "Q16570", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "LRG_801:g.6692C>T", "sequenceAccessionVersion": "LRG_801", "sequenceAccession": "LRG_801"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_801t1:c.265C>T", "sequenceAccessionVersion": "LRG_801t1", "sequenceAccession": "LRG_801t1"}, "proteinExpression": {"expression": "LRG_801p1:p.Arg89Cys", "sequenceAccessionVersion": "LRG_801p1", "sequenceAccession": "LRG_801p1", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA113789"}, {"db": "UniProtKB", "id": "Q16570#VAR_015068"}, {"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "34599082", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.00459, "source": "1000 Genomes Project", "minorAllele": "T"}, "alleleId": "33435", "variationId": "18396"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}], "traitSetId": "6213"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys) AND DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "accession": "RCV000000009", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "11369664", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8547665", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9399903", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9731074", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9746760", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9886340", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}]}], "type": "TYPE_DISEASE", "id": "6213", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2001-06-01T00:00:00Z", "dateCreated": "2017-12-15T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613665.0003_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "title": "ACKR1, ARG89CYS_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}, "clinvarAccession": {"accession": "SCV000020152", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-12-15T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Tournamille et al. (1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. They found that in some of these cases Fy(b-) individuals had the wildtype FY*B GATA but carried 271C-T and 304G-A mutations. The 271C-T substitution resulted in an R91C amino acid substitution (R89C in the predominant DARC isoform reported by Iwamoto et al. (1996)), which represented a considerable change of chemical nature, one that may affect the antigenic determinants of DARC, and thus may be of clinical significance. Parasol et al. (1998) noted that further studies were needed to determine whether erythrocytes carrying these mutations behave as Fy(bwk) variants."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9746760", "source": "PubMed"}]}, {"ids": [{"value": "8547665", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Carrington et al. (1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. (2001) showed that in both the CCR5 R60S and DARC R89C alleles, the loss of a positive charge from the intracellular loop leads to reduced surface expression, thereby identifying a novel mechanism that may be protective against disease: against malarial infection by Plasmodium vivax in the case of the DARC gene and against AIDS in the case of the CCR5 gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9399903", "source": "PubMed"}]}, {"ids": [{"value": "11369664", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "601373", "type": "MIM"}, {"db": "OMIM", "id": "609423", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "ACKR1"}], "names": [{"value": "ACKR1, ARG89CYS"}], "variantType": "Variation", "otherNames": [{"value": "ARG89CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20152"}], "traitMappings": [{"medgens": [{"name": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "cui": "C4017327"}], "clinicalAssertionId": "20152", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "mappingRef": "Preferred"}]}} +{"variationId": "18396", "variationName": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)", "variationType": "single nucleotide variant", "dateCreated": "2017-12-15T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "accession": "VCV000018396", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["1q23.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", 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"sequenceAccession": "NG_011626", "sequenceVersion": 3, "change": "g.6692C>T"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001122951.3:c.271C>T", "sequenceAccessionVersion": "NM_001122951.3", "sequenceAccession": "NM_001122951", "sequenceVersion": 3, "change": "c.271C>T"}, "proteinExpression": {"expression": "NP_001116423.1:p.Arg91Cys", "sequenceAccessionVersion": "NP_001116423.1", "sequenceAccession": "NP_001116423", "sequenceVersion": 1, "change": "p.Arg91Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_002036.4:c.265C>T", "sequenceAccessionVersion": "NM_002036.4", "sequenceAccession": "NM_002036", "sequenceVersion": 4, "change": "c.265C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_002027.2:p.Arg89Cys", "sequenceAccessionVersion": "NP_002027.2", "sequenceAccession": "NP_002027", "sequenceVersion": 2, "change": "p.Arg89Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"proteinExpression": {"expression": "Q16570:p.Arg89Cys", "sequenceAccessionVersion": "Q16570", "sequenceAccession": "Q16570", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "LRG_801:g.6692C>T", "sequenceAccessionVersion": "LRG_801", "sequenceAccession": "LRG_801"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_801t1:c.265C>T", "sequenceAccessionVersion": "LRG_801t1", "sequenceAccession": "LRG_801t1"}, "proteinExpression": {"expression": "LRG_801p1:p.Arg89Cys", "sequenceAccessionVersion": "LRG_801p1", "sequenceAccession": "LRG_801p1", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA113789"}, {"db": "UniProtKB", "id": "Q16570#VAR_015068"}, {"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "34599082", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.00459, "source": "1000 Genomes Project", "minorAllele": "T"}, "alleleId": "33435", "variationId": "18396"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}], "traitSetId": "6213"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys) AND DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "accession": "RCV000000009", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "11369664", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8547665", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9399903", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9731074", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9746760", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9886340", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}]}], "type": "TYPE_DISEASE", "id": "6213", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2001-06-01T00:00:00Z", "dateCreated": "2017-12-15T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613665.0003_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "title": "ACKR1, ARG89CYS_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}, "clinvarAccession": {"accession": "SCV000020152", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-12-15T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Tournamille et al. (1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. They found that in some of these cases Fy(b-) individuals had the wildtype FY*B GATA but carried 271C-T and 304G-A mutations. The 271C-T substitution resulted in an R91C amino acid substitution (R89C in the predominant DARC isoform reported by Iwamoto et al. (1996)), which represented a considerable change of chemical nature, one that may affect the antigenic determinants of DARC, and thus may be of clinical significance. Parasol et al. (1998) noted that further studies were needed to determine whether erythrocytes carrying these mutations behave as Fy(bwk) variants."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9746760", "source": "PubMed"}]}, {"ids": [{"value": "8547665", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Carrington et al. (1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. 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"HP:0001250"}]}, {"names": [{"value": "Delayed fine motor development", "type": "Preferred"}], "xrefs": [{"db": "HP", "id": "HP:0010862"}]}, {"names": [{"value": "Epileptic spasms", "type": "Preferred"}], "xrefs": [{"db": "HP", "id": "HP:0011097"}]}], "type": "TYPE_FINDING"}}], "simpleAllele": {"variantType": "copy number gain", "location": {"sequenceLocations": [{"assembly": "GRCh37", "chr": "CHROMOSOME_2", "innerStart": 86269067, "innerStop": 86509326}]}, "attributes": [{"attribute": {"base": {"value": "3"}, "type": "AbsoluteCopyNumber"}}]}, "traitSet": {"traits": [{"names": [{"value": "See Cases", "type": "Preferred"}]}], "type": "TYPE_FINDING"}, "id": "578243"}], "traitMappings": [{"medgens": [{"name": "Intellectual disability", "cui": "C3714756"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Intellectual disability", "mappingRef": "Preferred"}, {"medgens": [{"name": "Specific learning disability", "cui": "C4025790"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Specific learning disability", "mappingRef": "Preferred"}, {"medgens": [{"name": "Seizure", "cui": "C0036572"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Seizures", "mappingRef": "Preferred"}, {"medgens": [{"name": "Delayed gross motor development", "cui": "C1837658"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Delayed gross motor development", "mappingRef": "Preferred"}, {"medgens": [{"name": "Delayed speech and language development", "cui": "C0454644"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Delayed speech and language development", "mappingRef": "Preferred"}, {"medgens": [{"name": "See cases", "cui": "None"}], "clinicalAssertionId": "578243", "traitType": "PhenotypeInstruction", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "See Cases", "mappingRef": "Preferred"}, {"medgens": [{"name": "Constipation", "cui": "C0009806"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Constipation", "mappingRef": "Preferred"}, {"medgens": [{"name": "Dystonic disorder", "cui": "C0013421"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Dystonia", "mappingRef": "Preferred"}, {"medgens": [{"name": "Epileptic spasm", "cui": "C1527366"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Epileptic spasms", "mappingRef": "Preferred"}, {"medgens": [{"name": "Delayed fine motor development", "cui": "C4023681"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Delayed fine motor development", "mappingRef": "Preferred"}, {"medgens": [{"name": "Hypotonia", "cui": "C0026827"}], "clinicalAssertionId": "578243", "traitType": "Finding", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "Muscular hypotonia", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ten_records.xml/out.jsonl b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ten_records.xml/out.jsonl index 34ca9b0..eec7693 100644 --- a/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ten_records.xml/out.jsonl +++ b/tests/clinvar_data/snapshots/test_cli_data/test_convert_snapshot_to_jsonl/ten_records.xml/out.jsonl @@ -1,10 +1,10 @@ -{"variationId": "2", "variationName": "NM_014855.3(AP5Z1):c.80_83delinsTGCTGTAAACTGTAACTGTAAA (p.Arg27_Ile28delinsLeuLeuTer)", "variationType": "Indel", "dateCreated": "2017-01-30T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2021-05-16T00:00:00Z", "accession": "VCV000000002", "version": 3, "numberOfSubmitters": 2, "numberOfSubmissions": 2, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["7p22.1"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_7", "accession": "NC_000007.14", "start": 4775623, "stop": 4794397, "displayStart": 4775623, "displayStop": 4794397, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_7", "accession": "NC_000007.13", "start": 4815261, "stop": 4834025, "displayStart": 4815261, "displayStop": 4834025, "strand": "+"}]}], "omims": ["613653"], "fullName": "adaptor related protein complex 5 subunit zeta 1", "geneId": "9907", "hgncId": "HGNC:22197", "source": "submitted", "relationshipType": "GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE"}], "name": "NM_014855.3(AP5Z1):c.80_83delinsTGCTGTAAACTGTAACTGTAAA 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"AP5Z1, 4-BP DEL/22-BP INS, NT80_SPASTIC PARAPLEGIA 48, AUTOSOMAL RECESSIVE"}, "clinvarAccession": {"accession": "SCV000020155", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-01-30T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-06-29T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 French sibs with autosomal recessive spastic paraplegia-48 (SPG48; 613647), Slabicki et al. 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"xrefs": [{"db": "Genetic Alliance", "id": "Primary+autosomal+recessive+microcephaly+2/9156"}]}, {"value": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0011435"}]}], "symbols": [{"value": "MCPH2", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "604317", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "In WDR62 primary microcephaly (WDR62-MCPH), microcephaly (occipitofrontal circumference [OFC] = -2 SD) is usually present at birth, but in some instances becomes evident later in the first year of life. Growth is otherwise normal. Except for brain malformations in most affected individuals, no other congenital malformations are observed. Central nervous system involvement can include delayed motor development, mild-to-severe intellectual disability (ID), behavior problems, epilepsy, spasticity, and ataxia."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK578067"}]}], "citations": [{"ids": [{"value": "35188728", "source": "PubMed"}, {"value": "NBK578067", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "2512"}, {"db": "MedGen", "id": "C1858535"}, {"db": "MONDO", "id": "MONDO:0011435"}, {"db": "OMIM", "id": "604317", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "7167", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2010-09-09T00:00:00Z", "dateCreated": "2019-03-10T00:00:00Z", "mostRecentSubmission": "2019-03-10T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613583.0003_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "title": "WDR62, TRP224SER_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS"}, "clinvarAccession": {"accession": "SCV000020202", "version": 4, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2019-03-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-09-09T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 sibs and their cousin with microcephaly-2 and cortical malformations (MCPH2; 604317), Bilguvar et al. (2010) identified homozygosity for a missense mutation in the WDR62 gene, a G-to-C transversion in exon 6 that converted tryptophan to serine at codon 224 (W224S). All parents were heterozygous for the mutation, which was not identified in 1,290 Turkish and 1,500 Caucasian control chromosomes. Tryptophan-224 was invariant in all species examined from human to zebrafish and lamprey. The proband was a 6-year, 5-month-old boy who presented at 2 years of age with hyperactivity, seizures, and inability to sleep. He experienced 4 to 8 seizures per day and had microcephaly, micrognathia, and severe mental retardation, and could ambulate only with assistance. The sibs were cousins of the proband. One was an 8-year, 7-month-old female who presented at age 3 with seizures. She was microcephalic, hyperactive, and had dysconjugate gaze. She was able to walk independently and had no obvious dysmorphic features but had moderate mental retardation. Her brother was 12 years, 11 months old. He had seizures, self-mutilating behavior, and severe mental retardation, but could ambulate independently."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20729831", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "604317", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "WDR62"}], "names": [{"value": "WDR62, TRP224SER"}], "variantType": "Variation", "otherNames": [{"value": "TRP224SER", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613583.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20202"}], "traitMappings": [{"medgens": [{"name": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "cui": "C1858535"}], "clinicalAssertionId": "20202", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "mappingRef": "Preferred"}]}} -{"variationId": "40", "variationName": "NM_001083961.2(WDR62):c.4205_4208del (p.Val1402fs)", "variationType": "Deletion", "dateCreated": "2015-09-17T00:00:00Z", "dateLastUpdated": "2022-04-25T00:00:00Z", "mostRecentSubmission": "2015-09-17T00:00:00Z", "accession": "VCV000000040", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["19q13.12"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_19", "accession": "NC_000019.10", "start": 36054897, "stop": 36111145, "displayStart": 36054897, "displayStop": 36111145, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_19", "accession": "NC_000019.9", "start": 36545782, "stop": 36596011, "displayStart": 36545782, 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"G"}]}], "proteinChanges": ["V1397fs", "V1402fs"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "NG_028101.1:g.54689_54692del", "sequenceAccessionVersion": "NG_028101.1", "sequenceAccession": "NG_028101", "sequenceVersion": 1, "change": "g.54689_54692del"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001083961.2:c.4205_4208del", "sequenceAccessionVersion": "NM_001083961.2", "sequenceAccession": "NM_001083961", "sequenceVersion": 2, "change": "c.4205_4208del", "maneSelect": true}, "proteinExpression": {"expression": "NP_001077430.1:p.Val1402fs", "sequenceAccessionVersion": "NP_001077430.1", "sequenceAccession": "NP_001077430", "sequenceVersion": 1, "change": "p.Val1402fs"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001589", "type": "frameshift variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_173636.5:c.4190_4193del", "sequenceAccessionVersion": "NM_173636.5", "sequenceAccession": "NM_173636", "sequenceVersion": 5, "change": "c.4190_4193del"}, "proteinExpression": {"expression": "NP_775907.4:p.Val1397fs", "sequenceAccessionVersion": "NP_775907.4", "sequenceAccession": "NP_775907", "sequenceVersion": 4, "change": "p.Val1397fs"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001589", "type": "frameshift variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NC_000019.10:g.36104569_36104572del", "sequenceAccessionVersion": "NC_000019.10", "sequenceAccession": "NC_000019", "sequenceVersion": 10, "change": "g.36104569_36104572del"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NC_000019.9:g.36595471_36595474del", "sequenceAccessionVersion": "NC_000019.9", "sequenceAccession": "NC_000019", "sequenceVersion": 9, "change": "g.36595471_36595474del"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}], "xrefs": [{"db": "ClinGen", "id": "CA251360"}, {"db": "OMIM", "id": "613583.0001", "type": "Allelic variant"}, {"db": "dbSNP", "id": "397704721", "type": "rs"}], "alleleId": "15079", "variationId": "40"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "db": "MedGen", "id": "C1858535"}], "traitSetId": "7167"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2010-09-09T00:00:00Z", "submissionCount": 1}}}, "title": "NM_001083961.2(WDR62):c.4205_4208del (p.Val1402fs) AND Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "accession": "RCV000000057", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "20729831", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "613583.0005", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0003", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0004", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0009", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0001", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0010", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0013", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0002", "type": "Allelic variant"}, {"db": "OMIM", "id": "613583.0012", "type": "Allelic variant"}]}, {"value": "Primary autosomal recessive microcephaly 2", "type": "Alternate", "xrefs": [{"db": "Genetic Alliance", "id": "Primary+autosomal+recessive+microcephaly+2/9156"}]}, {"value": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "type": "Preferred", "xrefs": [{"db": "MONDO", "id": "MONDO:0011435"}]}], "symbols": [{"value": "MCPH2", "type": "Alternate", "xrefs": [{"db": "OMIM", "id": "604317", "type": "MIM"}]}], "attributes": [{"attribute": {"base": {"value": "In WDR62 primary microcephaly (WDR62-MCPH), microcephaly (occipitofrontal circumference [OFC] = -2 SD) is usually present at birth, but in some instances becomes evident later in the first year of life. Growth is otherwise normal. Except for brain malformations in most affected individuals, no other congenital malformations are observed. Central nervous system involvement can include delayed motor development, mild-to-severe intellectual disability (ID), behavior problems, epilepsy, spasticity, and ataxia."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK578067"}]}], "citations": [{"ids": [{"value": "35188728", "source": "PubMed"}, {"value": "NBK578067", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "2512"}, {"db": "MedGen", "id": "C1858535"}, {"db": "MONDO", "id": "MONDO:0011435"}, {"db": "OMIM", "id": "604317", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "7167", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2010-09-09T00:00:00Z", "dateCreated": "2015-09-17T00:00:00Z", "mostRecentSubmission": "2015-09-17T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613583.0001_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "title": "WDR62, 4-BP DEL, TGCC_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS"}, "clinvarAccession": {"accession": "SCV000020200", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-09-17T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": [{"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-09-09T00:00:00Z"}], "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 sibs with autosomal recessive microcephaly-2 and cortical malformations (MCPH2; 604317) and in an affected child from another family, all from consanguineous Turkish unions, Bilguvar et al. (2010) identified homozygosity for a 4-basepair deletion (TGCC) in exon 31 of the WDR62 gene. This deletion occurred at codon 1402 and resulted in a frameshift and premature termination (Val1402GlyfsTer12). The mutation was heterozygous in all parents. It was not observed in 1,290 Turkish control chromosomes. The index patient was a 4-year, 6-month-old female who initially presented at 4 months of age with small head size. At 2 years, 3 months she showed micrognathia and a bulbous nose, and suffered from severe mental retardation. She had had no seizures. MRI showed diffuse cortical thickening and pachygyria. The patient from the second family was a 2-year, 4 month-old male. He had microcephaly and developmental delay but no seizures. Coronal images of this patient showed findings of microlissencephaly including prominent microcephaly, bilateral Sylvian clefts, hypoplastic corpus callosum, and thickened cortex. The kinship coefficients between affected individuals from both families were consistent with fourth-degree relatedness."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20729831", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "604317", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "WDR62"}], "names": [{"value": "WDR62, 4-BP DEL, TGCC"}], "variantType": "Variation", "otherNames": [{"value": "4-BP DEL, TGCC", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613583.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20200"}], "traitMappings": [{"medgens": [{"name": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "cui": "C1858535"}], "clinicalAssertionId": "20200", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": 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"variantLength": 14, "positionVcf": 159175508, "referenceAlleleVcf": "CCCTGGCTGGCCTGT", "alternateAlleleVcf": "C"}]}], "otherNames": [{"value": "ACKR1, 14-BP DEL, NT286"}], "proteinChanges": ["W96fs", "W98fs"], "hgvsExpressions": [{"nucleotideExpression": {"expression": "LRG_801:g.6713_6726del", "sequenceAccessionVersion": "LRG_801", "sequenceAccession": "LRG_801"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_801t1:c.286_299del", "sequenceAccessionVersion": "LRG_801t1", "sequenceAccession": "LRG_801t1"}, "proteinExpression": {"expression": "LRG_801p1:p.Trp96fs", "sequenceAccessionVersion": "LRG_801p1", "sequenceAccession": "LRG_801p1", "change": "p.Trp96fs"}, "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NC_000001.10:g.159175515_159175528del", "sequenceAccessionVersion": "NC_000001.10", "sequenceAccession": "NC_000001", "sequenceVersion": 10, "change": "g.159175515_159175528del"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh37"}, {"nucleotideExpression": {"expression": "NC_000001.11:g.159205725_159205738del", "sequenceAccessionVersion": "NC_000001.11", "sequenceAccession": "NC_000001", "sequenceVersion": 11, "change": "g.159205725_159205738del"}, "type": "HGVS_TYPE_GENOMIC_TOP_LEVEL", "assembly": "GRCh38"}, {"nucleotideExpression": {"expression": "NG_011626.3:g.6713_6726del", "sequenceAccessionVersion": "NG_011626.3", "sequenceAccession": "NG_011626", "sequenceVersion": 3, "change": "g.6713_6726del"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "NM_001122951.3:c.292_305del", "sequenceAccessionVersion": "NM_001122951.3", "sequenceAccession": "NM_001122951", "sequenceVersion": 3, "change": "c.292_305del"}, "proteinExpression": {"expression": "NP_001116423.1:p.Trp98fs", "sequenceAccessionVersion": "NP_001116423.1", "sequenceAccession": "NP_001116423", "sequenceVersion": 1, "change": "p.Trp98fs"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001589", "type": "frameshift 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"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2000-04-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_002036.4(ACKR1):c.286_299del (p.Trp96fs) AND DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE", "accession": "RCV000000010", "version": 3}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "10791881", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "7669660", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8248172", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8547665", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "DUFFY NULL; Fy(a-b-)", "type": "Alternate"}, {"value": "DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": 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(1995) presented evidence for 2 different genetic backgrounds giving rise to the Fy(a-b-) phenotype. The most likely genetic mechanism in most individuals is downregulation of Duffy glycoprotein mRNA (see 613665.0002). However, the Duffy gene from a very rare Caucasian individual (AZ) with the Fy(a-b-) phenotype had a 14-bp deletion that resulted in a frameshift. In the Abstract and Results sections of their paper, Mallinson et al. (1995) reported that the deletion removed nucleotides 287 to 301 of DARC. However, their Figure 4 showed that the deletion involved nucleotides 292 to 305, which appeared to be correct. The DARC cDNA sequence used by Mallinson et al. (1995) was identical to that of the minor DARC variant reported by Chaudhuri et al. (1993). The frameshift resulting from the deletion introduced a stop codon 23 amino acids downstream and produced a putative truncated 118-amino acid protein. The occurrence of this mutation in an apparently healthy individual raised questions about the functional importance of the Duffy glycoprotein, not only in normal erythrocytes, but also in all human cells and tissues. The only known examples of the Fy(a-b-) phenotype in Caucasians were AZ and Czech gypsies."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "7669660", "source": "PubMed"}]}, {"ids": [{"value": "8248172", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Using the sequence of the major DARC variant reported by Iwamoto et al. 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"loss of function", "integerValue": "273"}, "type": "disease mechanism"}, "xrefs": [{"db": "Genetic Testing Registry (GTR)", "id": "GTR000561373"}]}, {"attribute": {"base": {"integerValue": "10738"}, "type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "10738"}]}], "citations": [{"ids": [{"value": "26401545", "source": "PubMed"}, {"value": "NBK316514", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "416"}, {"db": "Orphanet", "id": "93600"}, {"db": "MedGen", "id": "C3150878"}, {"db": "MONDO", "id": "MONDO:0013327"}, {"db": "OMIM", "id": "613616", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "19", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2010-09-10T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z", "mostRecentSubmission": "2013-04-04T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": 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"CA251361"}, {"db": "UniProtKB", "id": "O43379#VAR_063702"}, {"db": "OMIM", "id": "613583.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "267607176", "type": "rs"}], "alleleId": "15081", "variationId": "42"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "db": "MedGen", "id": "C1858535"}], "traitSetId": "7167"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2010-09-09T00:00:00Z", "submissionCount": 1}}}, "title": "NM_001083961.2(WDR62):c.671G>C (p.Trp224Ser) AND Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "accession": "RCV000000059", "version": 5}]}, "classifications": {"germlineClassification": {"reviewStatus": 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Growth is otherwise normal. Except for brain malformations in most affected individuals, no other congenital malformations are observed. 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Growth is otherwise normal. Except for brain malformations in most affected individuals, no other congenital malformations are observed. Central nervous system involvement can include delayed motor development, mild-to-severe intellectual disability (ID), behavior problems, epilepsy, spasticity, and ataxia."}, "type": "public definition"}, "xrefs": [{"db": "GeneReviews", "id": "NBK578067"}]}], "citations": [{"ids": [{"value": "35188728", "source": "PubMed"}, {"value": "NBK578067", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "Orphanet", "id": "2512"}, {"db": "MedGen", "id": "C1858535"}, {"db": "MONDO", "id": "MONDO:0011435"}, {"db": "OMIM", "id": "604317", "type": "MIM"}]}], "type": "TYPE_DISEASE", "id": "7167", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2010-09-09T00:00:00Z", "dateCreated": "2015-09-17T00:00:00Z", "mostRecentSubmission": "2015-09-17T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613583.0001_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "title": "WDR62, 4-BP DEL, TGCC_MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS"}, "clinvarAccession": {"accession": "SCV000020200", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2015-09-17T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2010-09-09T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "In 2 sibs with autosomal recessive microcephaly-2 and cortical malformations (MCPH2; 604317) and in an affected child from another family, all from consanguineous Turkish unions, Bilguvar et al. 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The kinship coefficients between affected individuals from both families were consistent with fourth-degree relatedness."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "20729831", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "604317", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "WDR62"}], "name": {"value": "WDR62, 4-BP DEL, TGCC"}, "variantType": "Variation", "otherNames": [{"value": "4-BP DEL, TGCC", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613583.0001", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH CORTICAL MALFORMATIONS", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20200"}], "traitMappings": [{"medgens": [{"name": "Microcephaly 2, primary, autosomal recessive, with or without cortical malformations", "cui": "C1858535"}], "clinicalAssertionId": "20200", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": 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(1995) presented evidence for 2 different genetic backgrounds giving rise to the Fy(a-b-) phenotype. The most likely genetic mechanism in most individuals is downregulation of Duffy glycoprotein mRNA (see 613665.0002). However, the Duffy gene from a very rare Caucasian individual (AZ) with the Fy(a-b-) phenotype had a 14-bp deletion that resulted in a frameshift. In the Abstract and Results sections of their paper, Mallinson et al. (1995) reported that the deletion removed nucleotides 287 to 301 of DARC. However, their Figure 4 showed that the deletion involved nucleotides 292 to 305, which appeared to be correct. The DARC cDNA sequence used by Mallinson et al. (1995) was identical to that of the minor DARC variant reported by Chaudhuri et al. (1993). The frameshift resulting from the deletion introduced a stop codon 23 amino acids downstream and produced a putative truncated 118-amino acid protein. 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(1996), as was recommended by Pogo and Chaudhuri (2000), this 14-bp deletion occurs at nucleotide 286."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "8547665", "source": "PubMed"}]}, {"ids": [{"value": "10791881", "source": "PubMed"}]}]}]}], "simpleAllele": {"genes": [{"symbol": "ACKR1"}], "name": {"value": "ACKR1, 14-BP DEL, NT286"}, "variantType": "Variation", "otherNames": [{"value": "14-BP DEL, NT286", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613665.0004", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20153"}], "traitMappings": [{"medgens": [{"name": "DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE", "cui": "C4017326"}], "clinicalAssertionId": "20153", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE", "mappingRef": "Preferred"}]}} +{"variationId": 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from ABHD12 (NG_028119.1), with insertion of GG", "dataSource": "NCBI curation", "type": "COMMENT_TYPE_PUBLIC"}, {"value": "The location of this deletion was determined from analysis of Fig. S4C in PubMed 20797687.", "dataSource": "NCBI curation", "type": "COMMENT_TYPE_PUBLIC"}], "alleleId": "15064", "variationId": "25"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "PHARC syndrome", "db": "MedGen", "id": "C2675204"}], "traitSetId": "17"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2010-09-10T00:00:00Z", "submissionCount": 1}}}, "title": "NM_015600.4(ABHD12):c.-6898_191+7002delinsCC AND PHARC syndrome", "accession": "RCV000000042", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", 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"NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)", "variationType": "single nucleotide variant", "dateCreated": "2017-12-15T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "accession": "VCV000018396", "version": 1, "numberOfSubmitters": 1, "numberOfSubmissions": 1, "recordType": "RECORD_TYPE_CLASSIFIED", "recordStatus": "RECORD_STATUS_CURRENT", "species": {"name": "Homo sapiens"}, "classifiedRecord": {"simpleAllele": {"genes": [{"locations": [{"cytogeneticLocations": ["1q23.2"], "sequenceLocations": [{"assembly": "GRCh38", "chr": "CHROMOSOME_1", "accession": "NC_000001.11", "start": 159204875, "stop": 159206500, "displayStart": 159204875, "displayStop": 159206500, "strand": "+"}, {"assembly": "GRCh37", "chr": "CHROMOSOME_1", "accession": "NC_000001.10", "start": 159173802, "stop": 159176289, "displayStart": 159173802, "displayStop": 159176289, "strand": "+"}]}], "omims": ["613665"], "fullName": "atypical chemokine receptor 1 (Duffy blood 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"NP_001116423.1:p.Arg91Cys", "sequenceAccessionVersion": "NP_001116423.1", "sequenceAccession": "NP_001116423", "sequenceVersion": 1, "change": "p.Arg91Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"nucleotideExpression": {"expression": "NM_002036.4:c.265C>T", "sequenceAccessionVersion": "NM_002036.4", "sequenceAccession": "NM_002036", "sequenceVersion": 4, "change": "c.265C>T", "maneSelect": true}, "proteinExpression": {"expression": "NP_002027.2:p.Arg89Cys", "sequenceAccessionVersion": "NP_002027.2", "sequenceAccession": "NP_002027", "sequenceVersion": 2, "change": "p.Arg89Cys"}, "molecularConsequences": [{"db": "SO", "id": "SO:0001583", "type": "missense variant"}], "type": "HGVS_TYPE_CODING"}, {"proteinExpression": {"expression": "Q16570:p.Arg89Cys", "sequenceAccessionVersion": "Q16570", "sequenceAccession": "Q16570", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_PROTEIN"}, {"nucleotideExpression": {"expression": "LRG_801:g.6692C>T", "sequenceAccessionVersion": "LRG_801", "sequenceAccession": "LRG_801"}, "type": "HGVS_TYPE_GENOMIC"}, {"nucleotideExpression": {"expression": "LRG_801t1:c.265C>T", "sequenceAccessionVersion": "LRG_801t1", "sequenceAccession": "LRG_801t1"}, "proteinExpression": {"expression": "LRG_801p1:p.Arg89Cys", "sequenceAccessionVersion": "LRG_801p1", "sequenceAccession": "LRG_801p1", "change": "p.Arg89Cys"}, "type": "HGVS_TYPE_CODING"}], "xrefs": [{"db": "ClinGen", "id": "CA113789"}, {"db": "UniProtKB", "id": "Q16570#VAR_015068"}, {"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "34599082", "type": "rs"}], "globalMinorAlleleFrequency": {"value": 0.00459, "source": "1000 Genomes Project", "minorAllele": "T"}, "alleleId": "33435", "variationId": "18396"}, "rcvList": {"rcvAccessions": [{"classifiedConditionList": {"classifiedConditions": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}], "traitSetId": "6213"}, "rcvClassifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": {"value": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z", "submissionCount": 1}}}, "title": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys) AND DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "accession": "RCV000000009", "version": 4}]}, "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Pathogenic", "citations": [{"ids": [{"value": "11369664", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8547665", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9399903", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9731074", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9746760", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9886340", "source": "PubMed"}], "type": "general"}], "conditions": [{"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred", "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}]}], "type": "TYPE_DISEASE", "id": "6213", "contributesToAggregateClassification": true}], "dateLastEvaluated": "2001-06-01T00:00:00Z", "dateCreated": "2017-12-15T00:00:00Z", "mostRecentSubmission": "2017-12-15T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "clinicalAssertions": [{"clinvarSubmissionId": {"localKey": "613665.0003_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "title": "ACKR1, ARG89CYS_DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE"}, "clinvarAccession": {"accession": "SCV000020152", "version": 3, "submitterIdentifiers": {"submitterName": "OMIM", "orgId": "3", "orgCategory": "resource"}, "dateUpdated": "2017-12-15T00:00:00Z", "dateCreated": "2013-04-04T00:00:00Z"}, "recordStatus": "RECORD_STATUS_CURRENT", "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2001-06-01T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [{"sample": {"origin": "ORIGIN_GERMLINE", "species": {"name": "human"}, "affectedStatus": "AFFECTED_STATUS_NOT_PROVIDED"}, "observedData": [{"attributes": [{"base": {"value": "Tournamille et al. (1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. They found that in some of these cases Fy(b-) individuals had the wildtype FY*B GATA but carried 271C-T and 304G-A mutations. The 271C-T substitution resulted in an R91C amino acid substitution (R89C in the predominant DARC isoform reported by Iwamoto et al. (1996)), which represented a considerable change of chemical nature, one that may affect the antigenic determinants of DARC, and thus may be of clinical significance. Parasol et al. (1998) noted that further studies were needed to determine whether erythrocytes carrying these mutations behave as Fy(bwk) variants."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9746760", "source": "PubMed"}]}, {"ids": [{"value": "8547665", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Carrington et al. (1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. (2001) showed that in both the CCR5 R60S and DARC R89C alleles, the loss of a positive charge from the intracellular loop leads to reduced surface expression, thereby identifying a novel mechanism that may be protective against disease: against malarial infection by Plasmodium vivax in the case of the DARC gene and against AIDS in the case of the CCR5 gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9399903", "source": "PubMed"}]}, {"ids": [{"value": "11369664", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "601373", "type": "MIM"}, {"db": "OMIM", "id": "609423", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "ACKR1"}], "name": {"value": "ACKR1, ARG89CYS"}, "variantType": "Variation", "otherNames": [{"value": "ARG89CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20152"}], "traitMappings": [{"medgens": [{"name": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "cui": "C4017327"}], "clinicalAssertionId": "20152", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_conversion_cli/test_cli_xml_to_json/one_record.jsonl b/tests/clinvar_data/snapshots/test_conversion_cli/test_cli_xml_to_json/one_record.jsonl index c81393a..5a42f3a 100644 --- a/tests/clinvar_data/snapshots/test_conversion_cli/test_cli_xml_to_json/one_record.jsonl +++ b/tests/clinvar_data/snapshots/test_conversion_cli/test_cli_xml_to_json/one_record.jsonl @@ -1 +1 @@ -{"variationId": "18396", "variationName": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)", "variationType": "single nucleotide variant", "dateCreated": "2017-12-15T00:00:00Z", "dateLastUpdated": "2023-12-25T00:00:00Z", "mostRecentSubmission": 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(1998) and Olsson et al. (1998) described a Duffy allele, FYB-weak (FYB-WK), or FYX, in approximately 3.5% of the population that, because of an arg89-to-cys (R89C) substitution in the first cytoplasmic domain of DARC, results in reduced levels of protein, lower antigen expression, and reduced ability to bind chemokines. The phenotype is called Fy(bwk), Fy(x), or either Fy(a-b+(weak)) or Fy(a+b+(weak)). The R89C substitution results from a C-to-T change at nucleotide 286 of the DARC gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9731074", "source": "PubMed"}]}, {"ids": [{"value": "9886340", "source": "PubMed"}]}]}, {"attributes": [{"base": {"value": "Parasol et al. (1998) noted that, in addition to West African blacks, the Duffy-null phenotype also occurs in non-Ashkenazi Jews, being found, for example, in approximately 20% of Jews from Yemen. 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(1997) described a CCR5 (601373) allele that carries a single amino acid substitution (R60S; 601373.0008) in the first intracellular domain of the protein that in heterozygous state appears to protect against human immunodeficiency virus (HIV) infection (see 609423). Tamasauskas et al. (2001) showed that in both the CCR5 R60S and DARC R89C alleles, the loss of a positive charge from the intracellular loop leads to reduced surface expression, thereby identifying a novel mechanism that may be protective against disease: against malarial infection by Plasmodium vivax in the case of the DARC gene and against AIDS in the case of the CCR5 gene."}, "type": "TYPE_DESCRIPTION"}], "citations": [{"ids": [{"value": "9399903", "source": "PubMed"}]}, {"ids": [{"value": "11369664", "source": "PubMed"}]}], "xrefs": [{"db": "OMIM", "id": "601373", "type": "MIM"}, {"db": "OMIM", "id": "609423", "type": "MIM"}]}]}], "simpleAllele": {"genes": [{"symbol": "ACKR1"}], "name": {"value": "ACKR1, ARG89CYS"}, "variantType": "Variation", "otherNames": [{"value": "ARG89CYS", "type": "NonHGVS"}], "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}]}, "traitSet": {"traits": [{"names": [{"value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "type": "Preferred"}]}], "type": "TYPE_DISEASE"}, "id": "20152"}], "traitMappings": [{"medgens": [{"name": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "cui": "C4017327"}], "clinicalAssertionId": "20152", "traitType": "Disease", "mappingType": "MAPPING_TYPE_NAME", "mappingValue": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", "mappingRef": "Preferred"}]}} diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/all/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/all/result index caf5f5d..44f3394 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/all/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/all/result @@ -8,17 +8,15 @@ "numberOfSubmitters": 2, "numberOfSubmissions": 3 }, - "somaticClinicalImpacts": [ - { - "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "description": "Tier I - Strong", - "dateLastEvaluated": "2024-01-24T00:00:00Z", - "dateCreated": "2024-03-05T00:00:00Z", - "mostRecentSubmission": "2024-03-05T00:00:00Z", - "numberOfSubmitters": 1, - "numberOfSubmissions": 3 - } - ], + "somaticClinicalImpact": { + "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "description": "Tier I - Strong", + "dateLastEvaluated": "2024-01-24T00:00:00Z", + "dateCreated": "2024-03-05T00:00:00Z", + "mostRecentSubmission": "2024-03-05T00:00:00Z", + "numberOfSubmitters": 1, + "numberOfSubmissions": 3 + }, "oncogenicityClassification": { "reviewStatus": "AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", "description": "Uncertain significance", diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/somatic/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/somatic/result index b49cf19..7b95f46 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/somatic/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_aggregate_classification_set_xmldict_data_to_pb/somatic/result @@ -1,13 +1,11 @@ { - "somaticClinicalImpacts": [ - { - "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "description": "Tier I - Strong", - "dateLastEvaluated": "2024-01-24T00:00:00Z", - "dateCreated": "2024-03-05T00:00:00Z", - "mostRecentSubmission": "2024-03-05T00:00:00Z", - "numberOfSubmitters": 1, - "numberOfSubmissions": 1 - } - ] + "somaticClinicalImpact": { + "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "description": "Tier I - Strong", + "dateLastEvaluated": "2024-01-24T00:00:00Z", + "dateCreated": "2024-03-05T00:00:00Z", + "mostRecentSubmission": "2024-03-05T00:00:00Z", + "numberOfSubmitters": 1, + "numberOfSubmissions": 1 + } } \ No newline at end of file diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_classified_record_xmldict_data_to_pb/id-15065/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_classified_record_xmldict_data_to_pb/id-15065/result index 7b756ed..9593279 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_classified_record_xmldict_data_to_pb/id-15065/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_classified_record_xmldict_data_to_pb/id-15065/result @@ -331,13 +331,11 @@ "dateCreated": "2013-04-04T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic", - "dateLastEvaluated": "2010-09-10T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic", + "dateLastEvaluated": "2010-09-10T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { @@ -385,11 +383,9 @@ "symbol": "ABHD12" } ], - "names": [ - { - "value": "ABHD12, 7-BP DUP, NT846" - } - ], + "name": { + "value": "ABHD12, 7-BP DUP, NT846" + }, "variantType": "Variation", "otherNames": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-20155/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-20155/result index 8b45f29..30d4420 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-20155/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-20155/result @@ -15,13 +15,11 @@ "dateCreated": "2013-04-04T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic", - "dateLastEvaluated": "2010-06-29T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic", + "dateLastEvaluated": "2010-06-29T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { @@ -69,11 +67,9 @@ "symbol": "AP5Z1" } ], - "names": [ - { - "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" - } - ], + "name": { + "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" + }, "variantType": "Variation", "otherNames": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-21727/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-21727/result index 6216c8b..396b66b 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-21727/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-21727/result @@ -22,13 +22,11 @@ "dateChanged": "2014-08-31T00:00:00Z" } ], - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic", - "dateLastEvaluated": "1991-09-15T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic", + "dateLastEvaluated": "1991-09-15T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { @@ -76,11 +74,9 @@ "symbol": "PKLR" } ], - "names": [ - { - "value": "PKLR, THR384MET" - } - ], + "name": { + "value": "PKLR, THR384MET" + }, "variantType": "Variation", "otherNames": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-2719824/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-2719824/result index 19772ef..9f04d86 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-2719824/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-2719824/result @@ -15,44 +15,42 @@ "dateCreated": "2020-07-16T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", - "germlineClassification": "Uncertain significance", - "citations": [ - { - "ids": [ - { - "value": "15888660", - "source": "PubMed" - } - ] - }, - { - "ids": [ - { - "value": "14729682", - "source": "PubMed" - } - ] - }, - { - "ids": [ - { - "value": "12891677", - "source": "PubMed" - } - ] - } - ], - "comments": [ - { - "value": "This sequence change replaces..." - } - ], - "dateLastEvaluated": "2019-08-08T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", + "germlineClassification": "Uncertain significance", + "citations": [ + { + "ids": [ + { + "value": "15888660", + "source": "PubMed" + } + ] + }, + { + "ids": [ + { + "value": "14729682", + "source": "PubMed" + } + ] + }, + { + "ids": [ + { + "value": "12891677", + "source": "PubMed" + } + ] + } + ], + "comments": [ + { + "value": "This sequence change replaces..." + } + ], + "dateLastEvaluated": "2019-08-08T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-3860220/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-3860220/result index 6a86113..36d8425 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-3860220/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinical_assertion_xmldict_data_to_pb/id-3860220/result @@ -26,12 +26,10 @@ } ], "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinvar_variation_release_xmldict_data_to_pb/VCV000000002/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinvar_variation_release_xmldict_data_to_pb/VCV000000002/result index f1f7b5a..8582491 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinvar_variation_release_xmldict_data_to_pb/VCV000000002/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_clinvar_variation_release_xmldict_data_to_pb/VCV000000002/result @@ -378,13 +378,11 @@ "dateCreated": "2013-04-04T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic", - "dateLastEvaluated": "2010-06-29T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic", + "dateLastEvaluated": "2010-06-29T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { @@ -432,11 +430,9 @@ "symbol": "AP5Z1" } ], - "names": [ - { - "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" - } - ], + "name": { + "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" + }, "variantType": "Variation", "otherNames": [ { @@ -484,12 +480,10 @@ "dateCreated": "2021-05-16T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", - "germlineClassification": "Pathogenic" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", + "germlineClassification": "Pathogenic" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [ { diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_haplotype_xmldict_data_to_pb/id-431012/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_haplotype_xmldict_data_to_pb/id-431012/result index 8906224..a9716c6 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_haplotype_xmldict_data_to_pb/id-431012/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_haplotype_xmldict_data_to_pb/id-431012/result @@ -561,14 +561,12 @@ "numberOfSubmitters": 0, "numberOfSubmissions": 0 }, - "somaticClinicalImpacts": [ - { - "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", - "description": "no classification for the single variant", - "numberOfSubmitters": 0, - "numberOfSubmissions": 0 - } - ], + "somaticClinicalImpact": { + "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", + "description": "no classification for the single variant", + "numberOfSubmitters": 0, + "numberOfSubmissions": 0 + }, "oncogenicityClassification": { "reviewStatus": "AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", "description": "no classification for the single variant", @@ -630,14 +628,12 @@ "numberOfSubmitters": 0, "numberOfSubmissions": 0 }, - "somaticClinicalImpacts": [ - { - "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", - "description": "no classification for the single variant", - "numberOfSubmitters": 0, - "numberOfSubmissions": 0 - } - ], + "somaticClinicalImpact": { + "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", + "description": "no classification for the single variant", + "numberOfSubmitters": 0, + "numberOfSubmissions": 0 + }, "oncogenicityClassification": { "reviewStatus": "AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", "description": "no classification for the single variant", diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_included_record_xmldict_data_to_pb/id-1054167/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_included_record_xmldict_data_to_pb/id-1054167/result index b426d51..8287b61 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_included_record_xmldict_data_to_pb/id-1054167/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_included_record_xmldict_data_to_pb/id-1054167/result @@ -331,14 +331,12 @@ "numberOfSubmitters": 0, "numberOfSubmissions": 0 }, - "somaticClinicalImpacts": [ - { - "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", - "description": "no classification for the single variant", - "numberOfSubmitters": 0, - "numberOfSubmissions": 0 - } - ], + "somaticClinicalImpact": { + "reviewStatus": "AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", + "description": "no classification for the single variant", + "numberOfSubmitters": 0, + "numberOfSubmissions": 0 + }, "oncogenicityClassification": { "reviewStatus": "AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT", "description": "no classification for the single variant", diff --git a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_variation_archive_xmldict_data_to_pb/VCV000000002/result b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_variation_archive_xmldict_data_to_pb/VCV000000002/result index e764500..2ff0009 100644 --- a/tests/clinvar_data/snapshots/test_conversion_data/test_convert_variation_archive_xmldict_data_to_pb/VCV000000002/result +++ b/tests/clinvar_data/snapshots/test_conversion_data/test_convert_variation_archive_xmldict_data_to_pb/VCV000000002/result @@ -375,13 +375,11 @@ "dateCreated": "2013-04-04T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "germlineClassification": "Pathogenic", - "dateLastEvaluated": "2010-06-29T00:00:00Z" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", + "germlineClassification": "Pathogenic", + "dateLastEvaluated": "2010-06-29T00:00:00Z" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "observedIns": [ { @@ -429,11 +427,9 @@ "symbol": "AP5Z1" } ], - "names": [ - { - "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" - } - ], + "name": { + "value": "AP5Z1, 4-BP DEL/22-BP INS, NT80" + }, "variantType": "Variation", "otherNames": [ { @@ -481,12 +477,10 @@ "dateCreated": "2021-05-16T00:00:00Z" }, "recordStatus": "RECORD_STATUS_CURRENT", - "classifications": [ - { - "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", - "germlineClassification": "Pathogenic" - } - ], + "classifications": { + "reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", + "germlineClassification": "Pathogenic" + }, "assertion": "ASSERTION_VARIATION_TO_DISEASE", "attributes": [ { diff --git a/tests/clinvar_data/test_conversion_data.py b/tests/clinvar_data/test_conversion_data.py index 5a65b45..453eee9 100644 --- a/tests/clinvar_data/test_conversion_data.py +++ b/tests/clinvar_data/test_conversion_data.py @@ -2205,7 +2205,7 @@ def test_convert_classification_scv_convert_classification_score(xml_str: str, e ], "dateLastEvaluated": "2024-01-24T00:00:00Z", "reviewStatus": "SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED", - "somaticClinicalImpacts": { + "somaticClinicalImpact": { "clinicalImpactAssertionType": "diagnostic", "clinicalImpactClinicalSignificance": "supports diagnosis", "value": "Tier I - Strong", @@ -3463,11 +3463,9 @@ def test_convert_allele_scv_convert_molecular_consequence(xml_str: str, expected "symbol": "THAP1", }, ], - "names": [ - { - "value": "THAP1, LYS24GLU", - }, - ], + "name": { + "value": "THAP1, LYS24GLU", + }, "otherNames": [ { "type": "NonHGVS", diff --git a/tests/clinvar_data/test_models_from_json.py b/tests/clinvar_data/test_models_from_json.py deleted file mode 100644 index a62b97c..0000000 --- a/tests/clinvar_data/test_models_from_json.py +++ /dev/null @@ -1,1920 +0,0 @@ -import datetime -import json - -import pytest - -from clinvar_data import conversion, models - - -def json_default(obj): - if isinstance(obj, datetime.datetime): - return obj.strftime("%Y-%m-%d %H:%M:%S") - elif isinstance(obj, datetime.date): - return obj.strftime("%Y-%m-%d") - else: - raise TypeError("Type not serializable") - - -def test_force_list_lst(): - assert models.force_list(1) == [1] - assert models.force_list([1]) == [1] - - -@pytest.mark.parametrize( - "input,expected", - [ - ( - {"@DB": "MedGen", "@ID": "C1704981"}, - {"db": "MedGen", "id": "C1704981"}, - ), - ( - { - "@DB": "MedGen", - "@ID": "C1704981", - "@Type": "CUI", - "@URL": "about:blank", - "@Status": "current", - }, - { - "db": "MedGen", - "id": "C1704981", - "type": "CUI", - "url": "about:blank", - "status": "current", - }, - ), - ], -) -def test_xref_type_from_json_data(input, expected): - obj = models.Xref.from_json_data(input) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ("affects", models.ClinicalSignificanceDescription.AFFECTS), - ("x", models.ClinicalSignificanceDescription.OTHER), - ], -) -def test_clinical_significance_description_from_the_wild(value, expected): - value = models.ClinicalSignificanceDescription.from_the_wild(value) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ("comment text", {"text": "comment text"}), - ({"#text": "comment text"}, {"text": "comment text"}), - ( - {"@DataSource": "NCBI curation", "@Type": "public", "#text": "comment text"}, - {"text": "comment text", "type": "public", "datasource": "NCBI curation"}, - ), - ], -) -def test_comment_from_json_data(value, expected): - obj = models.Comment.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ({"@Source": "PubMed", "#text": "9731074"}, {"source": "PubMed", "value": "9731074"}), - ({"@Source": "PubMed", "#text": "123"}, {"source": "PubMed", "value": "123"}), - ], -) -def test_citation_identifier_from_json_data(value, expected): - obj = models.CitationIdentifier.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Type": "general", "ID": {"@Source": "PubMed", "#text": "8547665"}}, - {"ids": [{"source": "PubMed", "value": "8547665"}], "type": "general"}, - ), - ({"CitationText": "text here"}, {"citation_text": "text here"}), - ( - { - "@Type": "review", - "@Abbrev": "GeneReviews", - "ID": [ - {"@Source": "PubMed", "#text": "29595935"}, - {"@Source": "BookShelf", "#text": "NBK488189"}, - ], - }, - { - "abbrev": "GeneReviews", - "ids": [ - {"source": "PubMed", "value": "29595935"}, - {"source": "BookShelf", "value": "NBK488189"}, - ], - "type": "review", - }, - ), - ( - {"URL": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=NEFL"}, - {"url": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=NEFL"}, - ), - ], -) -def test_citation_from_json_data(value, expected): - obj = models.Citation.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@type": "ACMG/ClinGen CNV Guidelines, 2019", "#text": "3"}, - {"type": "ACMG/ClinGen CNV Guidelines, 2019", "value": 3.0}, - ), - ({"@type": "Geneting testing", "#text": "5"}, {"type": "Geneting testing", "value": 5.0}), - ( - {"@type": "ACMG/ClinGen CNV Guidelines, 2019", "#text": "0.95"}, - {"type": "ACMG/ClinGen CNV Guidelines, 2019", "value": 0.95}, - ), - ], -) -def test_custom_assertion_score_from_json_data(value, expected): - obj = models.CustomAssertionScore.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@DateLastEvaluated": "2010-09-09", - "ReviewStatus": "no assertion criteria provided", - "Description": "Pathogenic", - }, - { - "date_last_evaluated": "2010-09-09", - "descriptions": ["pathogenic"], - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2020-01-06", - "ReviewStatus": "no assertion criteria provided", - "Description": "Benign", - "Comment": "comment text", - }, - { - "comments": [{"text": "comment text"}], - "date_last_evaluated": "2020-01-06", - "descriptions": ["benign"], - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2020-04-16", - "ReviewStatus": "no assertion criteria provided", - "Description": "Pathogenic", - "Citation": {"@Type": "general", "ID": {"@Source": "PubMed", "#text": "32576985"}}, - }, - { - "citations": [ - {"ids": [{"source": "PubMed", "value": "32576985"}], "type": "general"} - ], - "date_last_evaluated": "2020-04-16", - "descriptions": ["pathogenic"], - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2016-05-01", - "ReviewStatus": "no assertion criteria provided", - "Description": ["other", "other"], - "ExplanationOfInterpretation": "explanation text", - }, - { - "date_last_evaluated": "2016-05-01", - "descriptions": ["other", "other"], - "explanation_of_interpretation": "explanation text", - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2022-09-27", - "ReviewStatus": { - "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", - "#text": "criteria provided, single submitter", - }, - "Description": [ - { - "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", - "#text": "Pathogenic", - }, - { - "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", - "#text": "Pathogenic", - }, - ], - }, - { - "date_last_evaluated": "2022-09-27", - "descriptions": ["pathogenic", "pathogenic"], - "review_status": "criteria provided, single submitter", - }, - ), - ], -) -def test_clinical_significance_scv_from_json_data(value, expected): - obj = models.ClinicalSignificanceTypeSCV.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@DateLastEvaluated": "2010-09-09", - "ReviewStatus": "no assertion criteria provided", - "Description": "Pathogenic", - }, - { - "date_last_evaluated": "2010-09-09", - "description": "pathogenic", - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2020-01-06", - "ReviewStatus": "no assertion criteria provided", - "Description": "Benign", - "Comment": "comment text", - }, - { - "comments": [{"text": "comment text"}], - "date_last_evaluated": "2020-01-06", - "description": "benign", - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2020-04-16", - "ReviewStatus": "no assertion criteria provided", - "Description": "Pathogenic", - "Citation": {"@Type": "general", "ID": {"@Source": "PubMed", "#text": "32576985"}}, - }, - { - "citations": [ - {"ids": [{"source": "PubMed", "value": "32576985"}], "type": "general"} - ], - "date_last_evaluated": "2020-04-16", - "description": "pathogenic", - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2016-05-01", - "ReviewStatus": "no assertion criteria provided", - "Description": "other", - "ExplanationOfInterpretation": "explanation text", - }, - { - "date_last_evaluated": "2016-05-01", - "description": "other", - "explanation_of_interpretation": "explanation text", - "review_status": "no assertion criteria provided", - }, - ), - ( - { - "@DateLastEvaluated": "2022-09-27", - "ReviewStatus": { - "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", - "#text": "criteria provided, single submitter", - }, - "Description": { - "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", - "#text": "Pathogenic", - }, - }, - { - "date_last_evaluated": "2022-09-27", - "description": "pathogenic", - "review_status": "criteria provided, single submitter", - }, - ), - ], -) -def test_clinical_significance_rcv_from_json_data(value, expected): - obj = models.ClinicalSignificanceRCV.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Acc": "RCV000000009", - "@DateUpdated": "2022-04-23", - "@DateCreated": "2013-04-04", - "@Version": "4", - "@Type": "RCV", - }, - { - "acc": "RCV000000009", - "date_created": "2013-04-04", - "date_updated": "2022-04-23", - "type": "RCV", - "version": 4, - }, - ), - ], -) -def test_reference_clinvar_accession_from_json_data(value, expected): - obj = models.ReferenceClinVarAccession.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Attribute": { - "@Type": "ModeOfInheritance", - "@integerValue": "263", - "#text": "Autosomal recessive inheritance", - } - }, - { - "integer_value": 263, - "type": "ModeOfInheritance", - "value": "Autosomal recessive inheritance", - }, - ), - ( - { - "Attribute": { - "@Type": "ModeOfInheritance", - "@integerValue": "263", - "#text": "Autosomal recessive inheritance", - }, - "XRef": { - "@ID": "FGDYS-ID3", - "@DB": "Laboratory of Molecular ...", - }, - }, - { - "integer_value": 263, - "type": "ModeOfInheritance", - "value": "Autosomal recessive inheritance", - "xrefs": [{"db": "Laboratory of Molecular ...", "id": "FGDYS-ID3"}], - }, - ), - ], -) -def test_clinvar_accession_from_json_data(value, expected): - obj = models.ReferenceClinVarAssertionAttribute.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"Name": "ABCC8:c.2117-3C>T", "Zygosity": "SingleHeterozygote"}, - {"name": "ABCC8:c.2117-3C>T", "zygosity": "SingleHeterozygote"}, - ), - ( - { - "Name": "ABCC8:c.2117-3C>T", - "Zygosity": "SingleHeterozygote", - "RelativeOrientation": "cis", - }, - { - "name": "ABCC8:c.2117-3C>T", - "relative_orientation": "cis", - "zygosity": "SingleHeterozygote", - }, - ), - ], -) -def test_allele_description_from_json_data(value, expected): - obj = models.AlleleDescription.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Zygosity": "SingleHeterozygote", - "AlleleDescSet": [ - {"Name": "ABCC8:c.2117-3C>T", "Zygosity": "SingleHeterozygote"}, - {"Name": "KCNJ11:c.1009G>A", "Zygosity": "Homozygote"}, - ], - "Count": "1", - }, - { - "allele_descriptions": [ - {"name": "ABCC8:c.2117-3C>T", "zygosity": "SingleHeterozygote"}, - {"name": "KCNJ11:c.1009G>A", "zygosity": "Homozygote"}, - ], - "count": 1, - "zygosity": "SingleHeterozygote", - }, - ), - ( - { - "Zygosity": "SingleHeterozygote", - "AlleleDescSet": [], - }, - {"zygosity": "SingleHeterozygote"}, - ), - ( - {}, - None, - ), - ], -) -def test_cooccurrence_from_json_data(value, expected): - obj = models.Cooccurrence.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ("curation", models.ObservationMethod.CURATION), - ("x", models.ObservationMethod.OTHER), - ], -) -def test_observation_method_from_the_wild(value, expected): - value = models.ObservationMethod.from_the_wild(value) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Type": "Description", "#text": "Tournamille et al. (1998) ..."}, - {"type": "Description", "value": "Tournamille et al. (1998) ..."}, - ), - ], -) -def test_observed_data_attribute_from_json_data(value, expected): - obj = models.ObservedDataAttribute.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"Attribute": {"@Type": "Description", "#text": "not provided"}}, - {"attribute": {"type": "Description", "value": "not provided"}}, - ), - ( - { - "Attribute": { - "@Type": "Description", - "#text": "Tournamille et al. (1998) and Olsson et al. (1998)...", - }, - "Citation": [ - {"ID": {"@Source": "PubMed", "#text": "9731074"}}, - {"ID": {"@Source": "PubMed", "#text": "9886340"}}, - ], - }, - { - "attribute": { - "type": "Description", - "value": "Tournamille et al. (1998) and Olsson et al. " "(1998)...", - }, - "citations": [ - {"ids": [{"source": "PubMed", "value": "9731074"}]}, - {"ids": [{"source": "PubMed", "value": "9886340"}]}, - ], - }, - ), - ( - { - "Attribute": { - "@Type": "Description", - "#text": "In a patient with chronic hemolytic...", - }, - "Citation": {"ID": {"@Source": "PubMed", "#text": "6933565"}}, - "XRef": {"@DB": "OMIM", "@ID": "300653", "@Type": "MIM"}, - }, - { - "attribute": { - "type": "Description", - "value": "In a patient with chronic hemolytic...", - }, - "citations": [{"ids": [{"source": "PubMed", "value": "6933565"}]}], - "xrefs": [{"db": "OMIM", "id": "300653", "type": "MIM"}], - }, - ), - ], -) -def test_observed_data_from_json_data(value, expected): - obj = models.ObservedData.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Description": { - "@Type": "public", - "#text": "Phenotype: fine and gross motor delay...", - } - }, - {"description": {"text": "Phenotype: fine and gross motor delay...", "type": "public"}}, - ), - ], -) -def test_sample_description_from_json_data(value, expected): - obj = models.SampleDescription.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@NumFamiliesWithSegregationObserved": "1", - "@NumFamiliesWithVariant": "1", - "FamilyHistory": "yes", - }, - { - "family_history": "yes", - "num_families_with_segregation_observed": 1, - "num_families_with_variant": 1, - }, - ), - ( - {"@NumFamiliesWithVariant": "1", "FamilyHistory": "no"}, - {"family_history": "no", "num_families_with_variant": 1}, - ), - ], -) -def test_family_info_from_json_data(value, expected): - obj = models.FamilyInfo.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@TaxonomyId": "9606", "#text": "human"}, - {"taxonomy_id": 9606, "value": "human"}, - ), - ( - "human", - {"value": "human"}, - ), - ], -) -def test_species_from_json_data(value, expected): - obj = models.Species.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Type": "minimum", "@age_unit": "years", "#text": "10"}, - {"age_unit": "years", "type": "minimum", "value": 10}, - ), - ( - {"@Type": "maximum", "@age_unit": "years", "#text": "69"}, - {"age_unit": "years", "type": "maximum", "value": 69}, - ), - ( - {"@Type": "single", "@age_unit": "years", "#text": "80"}, - {"age_unit": "years", "type": "single", "value": 80}, - ), - ], -) -def test_age_from_json_data(value, expected): - obj = models.Age.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Type": "Preferred", "#text": "ACKR1"}, - {"type": "Preferred", "value": "ACKR1"}, - ), - ( - {"@Type": "Preferred", "#text": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)"}, - {"type": "Preferred", "value": "NM_002036.4(ACKR1):c.265C>T (p.Arg89Cys)"}, - ), - ( - {"@Type": "Alternate", "#text": "NM_001127505.2:c.155A>G(p.Tyr52Cys)"}, - {"type": "Alternate", "value": "NM_001127505.2:c.155A>G(p.Tyr52Cys)"}, - ), - ], -) -def test_typed_value_from_json_data(value, expected): - obj = models.TypedValue.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_006642.5(SDCCAG8):c.1946_1949del (p.Cys649fs)", - }, - "XRef": {"@ID": "CA113828", "@DB": "ClinGen"}, - }, - { - "value": { - "type": "Preferred", - "value": "NM_006642.5(SDCCAG8):c.1946_1949del (p.Cys649fs)", - }, - "xrefs": [{"db": "ClinGen", "id": "CA113828"}], - }, - ), - ], -) -def test_annotated_typed_value_from_json_data(value, expected): - obj = models.AnnotatedTypedValue.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@DataSource": "MedGen", "@ID": "CN192494"}, - {"data_source": "MedGen", "id": "CN192494"}, - ), - ( - {"@DataSource": "MedGen", "@ID": "CN192494", "@SourceType": "resource"}, - {"data_source": "MedGen", "id": "CN192494", "source_type": "resource"}, - ), - ], -) -def test_source_from_json_data(value, expected): - obj = models.Source.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Type": "co-occurring condition", "@ID": "70"}, - {"id": 70, "type": "co-occurring condition"}, - ), - ( - { - "@Type": "DrugResponseAndDisease", - "Name": {"ElementValue": {"@Type": "Preferred", "#text": "Breast Cancer"}}, - }, - { - "names": [{"value": {"type": "Preferred", "value": "Breast Cancer"}}], - "type": "DrugResponseAndDisease", - }, - ), - ( - {"@Type": "Finding member", "@ID": "890"}, - {"id": 890, "type": "Finding member"}, - ), - ], -) -def test_trait_relationship_from_json_data(value, expected): - obj = models.TraitRelationship.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"Name": {"ElementValue": {"@Type": "Preferred", "#text": "BARDET-BIEDL SYNDROME 16"}}}, - {"names": [{"value": {"type": "Preferred", "value": "BARDET-BIEDL SYNDROME 16"}}]}, - ), - ], -) -def test_clinvar_assertion_trait_relationship_from_json_data(value, expected): - obj = models.ClinVarAssertionTraitRelationship.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"Name": {"ElementValue": {"@Type": "Preferred", "#text": "BARDET-BIEDL SYNDROME 16"}}}, - {"names": [{"value": {"type": "Preferred", "value": "BARDET-BIEDL SYNDROME 16"}}]}, - ), - ], -) -def test_clinvar_assertion_trait_from_json_data(value, expected): - obj = models.ClinVarAssertionTrait.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@ID": "15693", - "@Type": "BloodGroup", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", - }, - "XRef": {"@Type": "Allelic variant", "@ID": "613665.0003", "@DB": "OMIM"}, - }, - }, - { - "names": [ - { - "value": { - "type": "Preferred", - "value": "DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE", - }, - "xrefs": [{"db": "OMIM", "id": "613665.0003", "type": "Allelic variant"}], - } - ], - "type": "BloodGroup", - }, - ), - ], -) -def test_trait_from_json_data(value, expected): - obj = models.Trait.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Type": "Indication", - "Trait": { - "@Type": "Finding", - "Name": {"ElementValue": {"@Type": "Preferred", "#text": "Diagnostic"}}, - }, - }, - { - "traits": [{"names": [{"value": {"type": "Preferred", "value": "Diagnostic"}}]}], - "type": "Indication", - }, - ), - ( - { - "@Type": "Indication", - "Trait": { - "@Type": "Finding", - "Name": {"ElementValue": {"@Type": "Preferred", "#text": "Vision phenotype"}}, - }, - }, - { - "traits": [ - {"names": [{"value": {"type": "Preferred", "value": "Vision phenotype"}}]} - ], - "type": "Indication", - }, - ), - ], -) -def test_indication_from_json_data(value, expected): - obj = models.Indication.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Origin": "germline", - "Species": {"@TaxonomyId": "9606", "#text": "human"}, - "AffectedStatus": "not provided", - }, - { - "affected_status": "not provided", - "origin": "germline", - "species": {"taxonomy_id": 9606, "value": "human"}, - }, - ), - ( - { - "Origin": "unknown", - "Species": {"@TaxonomyId": "9606", "#text": "human"}, - "AffectedStatus": "not provided", - "NumberTested": "3", - "NumberMales": "1", - "FamilyData": {"@NumFamilies": "1"}, - }, - { - "affected_status": "not provided", - "family_data": {"num_families": 1}, - "number_males": 1, - "number_tested": 3, - "origin": "unknown", - "species": {"taxonomy_id": 9606, "value": "human"}, - }, - ), - ], -) -def test_sample_from_json_data(value, expected): - obj = models.Sample.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Sample": { - "Origin": "germline", - "Species": "human", - "AffectedStatus": "not provided", - }, - "Method": {"MethodType": "literature only"}, - "ObservedData": [ - { - "Attribute": {"@Type": "Description", "#text": "In a 27-week-old male ..."}, - "Citation": {"ID": {"@Source": "PubMed", "#text": "19465910"}}, - "XRef": {"@DB": "OMIM", "@ID": "610031", "@Type": "MIM"}, - }, - { - "Attribute": { - "@Type": "Description", - "#text": "Fallet-Bianco et al. (2014)...", - }, - "Citation": {"ID": {"@Source": "PubMed", "#text": "25059107"}}, - }, - ], - }, - { - "methods": ["literature only"], - "observed_data": [ - { - "attribute": {"type": "Description", "value": "In a 27-week-old male ..."}, - "citations": [{"ids": [{"source": "PubMed", "value": "19465910"}]}], - "xrefs": [{"db": "OMIM", "id": "610031", "type": "MIM"}], - }, - { - "attribute": { - "type": "Description", - "value": "Fallet-Bianco et al. (2014)...", - }, - "citations": [{"ids": [{"source": "PubMed", "value": "25059107"}]}], - }, - ], - "sample": { - "affected_status": "not provided", - "origin": "germline", - "species": {"value": "human"}, - }, - }, - ), - ( - { - "Sample": { - "Origin": "germline", - "Species": {"@TaxonomyId": "9606", "#text": "human"}, - "AffectedStatus": "unknown", - "NumberTested": "1", - }, - "Method": {"MethodType": "clinical testing"}, - "ObservedData": { - "@ID": "110387662", - "Attribute": {"@integerValue": "1", "@Type": "VariantAlleles"}, - }, - }, - { - "methods": ["clinical testing"], - "observed_data": [{"attribute": {"integer_value": 1, "type": "VariantAlleles"}}], - "sample": { - "affected_status": "unknown", - "number_tested": 1, - "origin": "germline", - "species": {"taxonomy_id": 9606, "value": "human"}, - }, - }, - ), - ], -) -def test_observation_set_from_json_data(value, expected): - obj = models.ObservationSet.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Attribute": { - "@Accession": "NM_170784", - "@Version": "3", - "@Change": "c.281del", - "@Type": "HGVS, coding, RefSeq", - "@MANESelect": "true", - "#text": "NM_170784.3:c.281del", - } - }, - {"change": "c.281del", "type": "HGVS, coding, RefSeq", "value": "NM_170784.3:c.281del"}, - ), - ( - { - "Attribute": { - "@Accession": "NM_170784", - "@Version": "2", - "@Change": "c.281del", - "@Type": "HGVS, previous", - "#text": "NM_170784.2:c.281del", - } - }, - {"change": "c.281del", "type": "HGVS, previous", "value": "NM_170784.2:c.281del"}, - ), - ( - { - "Attribute": {"@Type": "MolecularConsequence", "#text": "frameshift variant"}, - "XRef": [ - {"@ID": "SO:0001589", "@DB": "Sequence Ontology"}, - {"@ID": "NM_018848.3:c.281del", "@DB": "RefSeq"}, - ], - }, - { - "type": "MolecularConsequence", - "value": "frameshift variant", - "xrefs": [ - {"db": "Sequence Ontology", "id": "SO:0001589"}, - {"db": "RefSeq", "id": "NM_018848.3:c.281del"}, - ], - }, - ), - ], -) -def test_measure_set_attribute_from_json_data(value, expected): - obj = models.MeasureSetAttribute.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Attribute": { - "@Accession": "LRG_801t1", - "@Type": "HGVS, coding, LRG", - "#text": "LRG_801t1:c.265C>T", - } - }, - {"type": "HGVS, coding, LRG", "value": "LRG_801t1:c.265C>T"}, - ), - ( - { - "Attribute": { - "@Accession": "NM_002036", - "@Version": "4", - "@Change": "c.286_299del", - "@Type": "HGVS, coding, RefSeq", - "@MANESelect": "true", - "#text": "NM_002036.4:c.286_299del", - } - }, - {"type": "HGVS, coding, RefSeq", "value": "NM_002036.4:c.286_299del"}, - ), - ], -) -def test_measure_type_attribute_from_json_data(value, expected): - obj = models.MeasureAttribute.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Value": "0.01099", - "@Source": "NHLBI Exome Sequencing Project (ESP) Exome Variant Server", - }, - { - "source": "NHLBI Exome Sequencing Project (ESP) Exome Variant Server", - "value": 0.01099, - }, - ), - ( - {"@Value": "0.00001", "@Source": "Exome Aggregation Consortium (ExAC)"}, - {"source": "Exome Aggregation Consortium (ExAC)", "value": 1e-05}, - ), - ], -) -def test_allele_frequency_from_json_data(value, expected): - obj = models.AlleleFrequency.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - {"@Value": "0.00459", "@Source": "1000 Genomes Project", "@MinorAllele": "T"}, - {"minor_allele": "T", "source": "1000 Genomes Project", "value": 0.00459}, - ), - ( - {"@Value": "0.00080", "@Source": "1000 Genomes Project", "@MinorAllele": "A"}, - {"minor_allele": "A", "source": "1000 Genomes Project", "value": 0.0008}, - ), - ], -) -def test_global_minor_allele_frequency_from_json_data(value, expected): - obj = models.GlobalMinorAlleleFrequency.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Acc": "SCV000020152", - "@DateCreated": "2013-04-04", - "@DateUpdated": "2017-12-15", - "@Version": "3", - "@Type": "SCV", - "@OrgID": "3", - "@OrganizationCategory": "resource", - "@OrgType": "primary", - }, - { - "acc": "SCV000020152", - "date_created": "2013-04-04", - "date_updated": "2017-12-15", - "org_category": "resource", - "org_id": "3", - "org_type": "primary", - "type": "SCV", - "version": 3, - }, - ), - ], -) -def test_clinvar_assertion_accession_from_json_data(value, expected): - obj = models.ClinVarAssertionAccession.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "16", - "@Accession": "NC_000016.10", - "@start": "50742086", - "@stop": "50801935", - "@display_start": "50742086", - "@display_stop": "50801935", - "@Strand": "+", - }, - { - "accession": "NC_000016.10", - "assembly": "GRCh38", - "assembly_accession_version": "GCF_000001405.38", - "assembly_status": "current", - "chr": "16", - "display_start": 50742086, - "display_stop": 50801935, - "start": 50742086, - "stop": 50801935, - "strand": "+", - }, - ), - ( - { - "@Assembly": "GRCh37", - "@AssemblyAccessionVersion": "GCF_000001405.25", - "@AssemblyStatus": "previous", - "@Chr": "6", - "@Accession": "NC_000006.11", - "@start": "41129260", - "@stop": "41129260", - "@display_start": "41129260", - "@display_stop": "41129260", - "@variantLength": "1", - "@positionVCF": "41129260", - "@referenceAlleleVCF": "C", - "@alternateAlleleVCF": "T", - }, - { - "accession": "NC_000006.11", - "alternate_allele_vcf": "T", - "assembly": "GRCh37", - "assembly_accession_version": "GCF_000001405.25", - "assembly_status": "previous", - "chr": "6", - "display_start": 41129260, - "display_stop": 41129260, - "position_vcf": 41129260, - "reference_allele_vcf": "C", - "start": 41129260, - "stop": 41129260, - "variant_length": 1, - }, - ), - ], -) -def test_sequence_location_from_json_data(value, expected): - obj = models.SequenceLocation.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "Attribute": { - "@dateValue": "2020-05-27", - "@Type": "Haploinsufficiency", - "#text": "Little evidence for dosage pathogenicity", - }, - "Citation": { - "URL": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - }, - }, - { - "citations": [ - { - "url": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - } - ], - "date_value": "2020-05-27", - "type": "Haploinsufficiency", - "value": "Little evidence for dosage pathogenicity", - }, - ), - ( - { - "Attribute": { - "@dateValue": "2020-05-27", - "@Type": "Triplosensitivity", - "#text": "No evidence available", - }, - "Citation": { - "URL": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - }, - }, - { - "citations": [ - { - "url": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - } - ], - "date_value": "2020-05-27", - "type": "Triplosensitivity", - "value": "No evidence available", - }, - ), - ], -) -def test_measure_relationship_attribute_from_json_data(value, expected): - obj = models.MeasureRelationshipAttribute.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value", - [ - { - "@Type": "within single gene", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "TGF-beta activated kinase 1 (MAP3K7) binding protein 2", - } - }, - "Symbol": {"ElementValue": {"@Type": "Preferred", "#text": "TAB2"}}, - "AttributeSet": [ - { - "Attribute": { - "@dateValue": "2020-05-27", - "@Type": "Haploinsufficiency", - "#text": "Little evidence for dosage pathogenicity", - }, - "Citation": { - "URL": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - }, - }, - { - "Attribute": { - "@dateValue": "2020-05-27", - "@Type": "Triplosensitivity", - "#text": "No evidence available", - }, - "Citation": { - "URL": "https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=TAB2" - }, - }, - ], - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "6", - "@Accession": "NC_000006.12", - "@start": "149217926", - "@stop": "149411607", - "@display_start": "149217926", - "@display_stop": "149411607", - "@Strand": "+", - }, - ], - "XRef": [ - {"@ID": "23118", "@DB": "Gene"}, - ], - }, - ], -) -def test_measure_relationship_from_json_data(value, snapshot): - obj = models.MeasureRelationship.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - # NB: the input/expect output value pairs do not fit on one screen any more for - # this test, so we use snapshot testing - snapshot.assert_match(json.dumps(value, indent=2), "output") - - -@pytest.mark.parametrize( - "value", - [ - { - "@Type": "Deletion", - "@ID": "33436", - "Name": [ - { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_002036.4(ACKR1):c.286_299del (p.Trp96fs)", - } - }, - { - "ElementValue": {"@Type": "Alternate", "#text": "ACKR1, 14-BP DEL, NT286"}, - "XRef": {"@Type": "Allelic variant", "@ID": "613665.0004", "@DB": "OMIM"}, - }, - ], - "CanonicalSPDI": "NC_000001.11:159205718:CCTGGCTGGCCTGTCCTGGC:CCTGGC", - "AttributeSet": [ - { - "Attribute": { - "@Accession": "LRG_801t1", - "@Type": "HGVS, coding, LRG", - "#text": "LRG_801t1:c.286_299del", - } - }, - ], - "CytogeneticLocation": "1q23.2", - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "1", - "@Accession": "NC_000001.11", - "@start": "159205719", - "@stop": "159205732", - "@display_start": "159205719", - "@display_stop": "159205732", - "@variantLength": "14", - "@positionVCF": "159205718", - "@referenceAlleleVCF": "CCCTGGCTGGCCTGT", - "@alternateAlleleVCF": "C", - }, - ], - "MeasureRelationship": { - "@Type": "within single gene", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "atypical chemokine receptor 1 (Duffy blood group)", - } - }, - "Symbol": {"ElementValue": {"@Type": "Preferred", "#text": "ACKR1"}}, - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "1", - "@Accession": "NC_000001.11", - "@start": "159204875", - "@stop": "159206500", - "@display_start": "159204875", - "@display_stop": "159206500", - "@Strand": "+", - }, - ], - "XRef": [ - {"@ID": "2532", "@DB": "Gene"}, - ], - }, - "XRef": [ - {"@Type": "Allelic variant", "@ID": "613665.0004", "@DB": "OMIM"}, - ], - } - ], -) -def test_measure_from_json_data(value, snapshot): - obj = models.Measure.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - # NB: the input/expect output value pairs do not fit on one screen any more for - # this test, so we use snapshot testing - snapshot.assert_match(json.dumps(value, indent=2), "output") - - -@pytest.mark.parametrize( - "value", - [ - { - "@Type": "Variant", - "@ID": "18397", - "@Acc": "VCV000018397", - "@Version": "1", - "Measure": { - "@Type": "Deletion", - "@ID": "33436", - "Name": [ - { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_002036.4(ACKR1):c.286_299del (p.Trp96fs)", - } - }, - { - "ElementValue": {"@Type": "Alternate", "#text": "ACKR1, 14-BP DEL, NT286"}, - "XRef": {"@Type": "Allelic variant", "@ID": "613665.0004", "@DB": "OMIM"}, - }, - ], - "CanonicalSPDI": "NC_000001.11:159205718:CCTGGCTGGCCTGTCCTGGC:CCTGGC", - "AttributeSet": [ - { - "Attribute": { - "@Accession": "LRG_801t1", - "@Type": "HGVS, coding, LRG", - "#text": "LRG_801t1:c.286_299del", - } - }, - ], - "CytogeneticLocation": "1q23.2", - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "1", - "@Accession": "NC_000001.11", - "@start": "159205719", - "@stop": "159205732", - "@display_start": "159205719", - "@display_stop": "159205732", - "@variantLength": "14", - "@positionVCF": "159205718", - "@referenceAlleleVCF": "CCCTGGCTGGCCTGT", - "@alternateAlleleVCF": "C", - }, - ], - "MeasureRelationship": { - "@Type": "within single gene", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "atypical chemokine receptor 1 (Duffy blood group)", - } - }, - "Symbol": {"ElementValue": {"@Type": "Preferred", "#text": "ACKR1"}}, - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "1", - "@Accession": "NC_000001.11", - "@start": "159204875", - "@stop": "159206500", - "@display_start": "159204875", - "@display_stop": "159206500", - "@Strand": "+", - }, - ], - "XRef": [ - {"@ID": "2532", "@DB": "Gene"}, - ], - }, - "XRef": [ - {"@Type": "Allelic variant", "@ID": "613665.0004", "@DB": "OMIM"}, - ], - }, - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_002036.4(ACKR1):c.286_299del (p.Trp96fs)", - } - }, - "XRef": {"@ID": "CA113791", "@DB": "ClinGen"}, - }, - ], -) -def test_measure_set_from_json_data(value, snapshot): - obj = models.MeasureSet.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - snapshot.assert_match(json.dumps(value, indent=2), "output") - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Type": "CompoundHeterozygote", - "MeasureSet": [ - { - "@Type": "Variant", - "Measure": { - "@Type": "Variation", - "AttributeSet": { - "Attribute": {"@Type": "HGVS", "#text": "NM_000497.3:c.1024C>T"} - }, - "MeasureRelationship": { - "@Type": "variant in gene", - "Symbol": { - "ElementValue": {"@Type": "Preferred", "#text": "CYP11B1"} - }, - }, - }, - }, - { - "@Type": "Variant", - "Measure": { - "@Type": "Variation", - "AttributeSet": { - "Attribute": {"@Type": "HGVS", "#text": "NM_000497.3:c.1012dup"} - }, - "MeasureRelationship": { - "@Type": "variant in gene", - "Symbol": { - "ElementValue": {"@Type": "Preferred", "#text": "CYP11B1"} - }, - }, - }, - }, - ], - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_000497.3:c.[1024C>T];[1012dup]", - } - }, - }, - { - "measures": [ - { - "measures": [ - { - "attributes": [{"type": "HGVS", "value": "NM_000497.3:c.1024C>T"}], - "measure_relationship": [ - { - "symbols": [ - {"value": {"type": "Preferred", "value": "CYP11B1"}} - ], - "type": "variant in " "gene", - } - ], - "type": "variation", - } - ], - "type": "Variant", - }, - { - "measures": [ - { - "attributes": [{"type": "HGVS", "value": "NM_000497.3:c.1012dup"}], - "measure_relationship": [ - { - "symbols": [ - {"value": {"type": "Preferred", "value": "CYP11B1"}} - ], - "type": "variant in " "gene", - } - ], - "type": "variation", - } - ], - "type": "Variant", - }, - ], - "names": [ - {"value": {"type": "Preferred", "value": "NM_000497.3:c.[1024C>T];[1012dup]"}} - ], - "type": "CompoundHeterozygote", - }, - ) - ], -) -def test_genotype_set_from_json_data(value, expected): - obj = models.GenotypeSet.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@Type": "Disease", - "Trait": { - "@Type": "Disease", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "BARDET-BIEDL SYNDROME 2/6, DIGENIC", - } - }, - }, - }, - { - "traits": [ - { - "names": [ - { - "value": { - "type": "Preferred", - "value": "BARDET-BIEDL SYNDROME 2/6, " "DIGENIC", - } - } - ], - "type": "Disease", - } - ], - "type": "Disease", - }, - ) - ], -) -def test_trait_set_from_json_data(value, expected): - obj = models.TraitSet.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected - - -@pytest.mark.parametrize( - "value", - [ - { - "@ID": "63146", - "@DateLastUpdated": "2022-04-23", - "@DateCreated": "2013-04-04", - "ClinVarAccession": { - "@Acc": "RCV000005643", - "@DateUpdated": "2022-04-23", - "@DateCreated": "2013-04-04", - "@Version": "4", - "@Type": "RCV", - }, - "RecordStatus": "current", - "ClinicalSignificance": { - "@DateLastEvaluated": "2001-09-21", - "ReviewStatus": "no assertion criteria provided", - "Description": "Pathogenic", - }, - "Assertion": {"@Type": "variation to disease"}, - "ObservedIn": { - "Sample": { - "Origin": "germline", - "Species": {"@TaxonomyId": "9606", "#text": "human"}, - "AffectedStatus": "not provided", - }, - "Method": {"MethodType": "literature only"}, - "ObservedData": { - "@ID": "96578166", - "Attribute": { - "@Type": "Description", - "#text": "In a patient carrying 2 different termination codons in the BBS2 gene (606151.0003, 606151.0004), Katsanis et al. (2001) identified a nonsense mutation in the BBS6 gene, a glutamine-to-termination substitution at codon 147.", - }, - "Citation": { - "@Type": "general", - "ID": {"@Source": "PubMed", "#text": "11567139"}, - }, - }, - }, - "MeasureSet": { - "@Type": "Variant", - "@ID": "5318", - "@Acc": "VCV000005318", - "@Version": "1", - "Measure": { - "@Type": "single nucleotide variant", - "@ID": "20357", - "Name": [ - { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_170784.3(MKKS):c.442C>T (p.Gln148Ter)", - } - }, - { - "ElementValue": {"@Type": "Alternate", "#text": "Q147*"}, - "XRef": { - "@Type": "Allelic variant", - "@ID": "604896.0012", - "@DB": "OMIM", - }, - }, - ], - "CanonicalSPDI": "NC_000020.11:10413072:G:A", - "AttributeSet": [ - { - "Attribute": { - "@Accession": "NM_018848", - "@Version": "3", - "@Change": "c.442C>T", - "@Type": "HGVS, coding, RefSeq", - "#text": "NM_018848.3:c.442C>T", - } - }, - { - "Attribute": { - "@Accession": "NM_170784", - "@Version": "3", - "@Change": "c.442C>T", - "@Type": "HGVS, coding, RefSeq", - "@MANESelect": "true", - "#text": "NM_170784.3:c.442C>T", - } - }, - { - "Attribute": { - "@Accession": "NG_009109", - "@Version": "2", - "@Change": "g.26146C>T", - "@Type": "HGVS, genomic, RefSeqGene", - "#text": "NG_009109.2:g.26146C>T", - } - }, - { - "Attribute": { - "@Accession": "NC_000020", - "@Version": "11", - "@Change": "g.10413073G>A", - "@Type": "HGVS, genomic, top level", - "@integerValue": "38", - "#text": "NC_000020.11:g.10413073G>A", - } - }, - { - "Attribute": { - "@Accession": "NC_000020", - "@Version": "10", - "@Change": "g.10393721G>A", - "@Type": "HGVS, genomic, top level, previous", - "@integerValue": "37", - "#text": "NC_000020.10:g.10393721G>A", - } - }, - { - "Attribute": { - "@Accession": "NP_061336", - "@Version": "1", - "@Change": "p.Gln148Ter", - "@Type": "HGVS, protein, RefSeq", - "#text": "NP_061336.1:p.Gln148Ter", - } - }, - { - "Attribute": { - "@Accession": "NP_740754", - "@Version": "1", - "@Change": "p.Gln148Ter", - "@Type": "HGVS, protein, RefSeq", - "#text": "NP_740754.1:p.Gln148Ter", - } - }, - { - "Attribute": {"@Type": "MolecularConsequence", "#text": "nonsense"}, - "XRef": [ - {"@ID": "SO:0001587", "@DB": "Sequence Ontology"}, - {"@ID": "NM_018848.3:c.442C>T", "@DB": "RefSeq"}, - ], - }, - { - "Attribute": {"@Type": "MolecularConsequence", "#text": "nonsense"}, - "XRef": [ - {"@ID": "SO:0001587", "@DB": "Sequence Ontology"}, - {"@ID": "NM_170784.3:c.442C>T", "@DB": "RefSeq"}, - ], - }, - {"Attribute": {"@Type": "ProteinChange1LetterCode", "#text": "Q148*"}}, - {"Attribute": {"@Type": "ProteinChange3LetterCode", "#text": "GLN147TER"}}, - ], - "CytogeneticLocation": "20p12.2", - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "20", - "@Accession": "NC_000020.11", - "@start": "10413073", - "@stop": "10413073", - "@display_start": "10413073", - "@display_stop": "10413073", - "@variantLength": "1", - "@positionVCF": "10413073", - "@referenceAlleleVCF": "G", - "@alternateAlleleVCF": "A", - }, - { - "@Assembly": "GRCh37", - "@AssemblyAccessionVersion": "GCF_000001405.25", - "@AssemblyStatus": "previous", - "@Chr": "20", - "@Accession": "NC_000020.10", - "@start": "10393721", - "@stop": "10393721", - "@display_start": "10393721", - "@display_stop": "10393721", - "@variantLength": "1", - "@positionVCF": "10393721", - "@referenceAlleleVCF": "G", - "@alternateAlleleVCF": "A", - }, - ], - "MeasureRelationship": { - "@Type": "within single gene", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "MKKS centrosomal shuttling protein", - } - }, - "Symbol": {"ElementValue": {"@Type": "Preferred", "#text": "MKKS"}}, - "SequenceLocation": [ - { - "@Assembly": "GRCh38", - "@AssemblyAccessionVersion": "GCF_000001405.38", - "@AssemblyStatus": "current", - "@Chr": "20", - "@Accession": "NC_000020.11", - "@start": "10401009", - "@stop": "10434222", - "@display_start": "10401009", - "@display_stop": "10434222", - "@Strand": "-", - }, - { - "@Assembly": "GRCh37", - "@AssemblyAccessionVersion": "GCF_000001405.25", - "@AssemblyStatus": "previous", - "@Chr": "20", - "@Accession": "NC_000020.10", - "@start": "10385427", - "@stop": "10414886", - "@display_start": "10385427", - "@display_stop": "10414886", - "@variantLength": "29460", - "@Strand": "-", - }, - ], - "XRef": [ - {"@ID": "8195", "@DB": "Gene"}, - {"@Type": "MIM", "@ID": "604896", "@DB": "OMIM"}, - {"@ID": "HGNC:7108", "@DB": "HGNC"}, - ], - }, - "XRef": [ - {"@Type": "Allelic variant", "@ID": "604896.0012", "@DB": "OMIM"}, - {"@Type": "rs", "@ID": "137853154", "@DB": "dbSNP"}, - ], - }, - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "NM_170784.3(MKKS):c.442C>T (p.Gln148Ter)", - } - }, - "XRef": {"@ID": "CA117400", "@DB": "ClinGen"}, - }, - "TraitSet": { - "@Type": "Disease", - "@ID": "19803", - "Trait": { - "@ID": "32093", - "@Type": "Disease", - "Name": { - "ElementValue": { - "@Type": "Preferred", - "#text": "Bardet-biedl syndrome 2/6, digenic", - } - }, - "XRef": {"@ID": "C4016908", "@DB": "MedGen"}, - }, - }, - } - ], -) -def test_reference_clinvar_assertion_from_json_data(value, snapshot): - obj = models.ReferenceClinVarAssertion.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - snapshot.assert_match(json.dumps(value, indent=2, default=json_default), "output") - - -@pytest.mark.parametrize( - "value,expected", - [ - ( - { - "@localKey": "604896.0012_BARDET-BIEDL SYNDROME 2/6, DIGENIC", - "@submitter": "OMIM", - "@submitterDate": "2017-12-13", - "@title": "MKKS, GLN147TER_BARDET-BIEDL SYNDROME 2/6, DIGENIC", - }, - { - "local_key": "604896.0012_BARDET-BIEDL SYNDROME 2/6, DIGENIC", - "submitter": "OMIM", - "submitter_date": "2017-12-13", - "title": "MKKS, GLN147TER_BARDET-BIEDL SYNDROME 2/6, DIGENIC", - }, - ), - ], -) -def test_clinvar_submission_id_from_json_data(value, expected): - obj = models.ClinVarSubmissionId.from_json_data(value) - value = conversion.remove_empties_from_containers(obj.model_dump(mode="json")) - assert value == expected