diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java index 4d343236d94..1a03b91878d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java @@ -47,7 +47,8 @@ public class GencodeFuncotation implements Funcotation { private String annotationTranscript; // TRIVIAL private String transcriptStrand; // TRIVIAL private Integer transcriptExon; // CDS / UTRs - private Integer transcriptPos; // TRIVIAL + private Integer transcriptStartPos; // TRIVIAL + private Integer transcriptEndPos; // TRIVIAL private String cDnaChange; // CDS private String codonChange; // CDS private String proteinChange; // CDS @@ -131,7 +132,8 @@ public class GencodeFuncotation implements Funcotation { this.annotationTranscript = that.annotationTranscript; this.transcriptStrand = that.transcriptStrand; this.transcriptExon = that.transcriptExon; - this.transcriptPos = that.transcriptPos; + this.transcriptStartPos = that.transcriptStartPos; + this.transcriptEndPos = that.transcriptEndPos; this.cDnaChange = that.cDnaChange; this.codonChange = that.codonChange; this.proteinChange = that.proteinChange; @@ -294,7 +296,7 @@ public String getField(final String fieldName) { case "transcriptExon": return (transcriptExonSerializedOverride != null ? transcriptExonSerializedOverride : (transcriptExon != null ? String.valueOf(transcriptExon) : "")); case "transcriptPos": - return (transcriptPosSerializedOverride != null ? transcriptPosSerializedOverride : (transcriptPos != null ? String.valueOf(transcriptPos) : "")); + return (transcriptPosSerializedOverride != null ? transcriptPosSerializedOverride : getTranscriptPosString()); case "cDnaChange": return (cDnaChangeSerializedOverride != null ? cDnaChangeSerializedOverride : (cDnaChange != null ? cDnaChange : "")); case "codonChange": @@ -353,7 +355,9 @@ public boolean equals(final Object o) { return false; if (transcriptExon != null ? !transcriptExon.equals(that.transcriptExon) : that.transcriptExon != null) return false; - if (transcriptPos != null ? !transcriptPos.equals(that.transcriptPos) : that.transcriptPos != null) + if (transcriptStartPos != null ? !transcriptStartPos.equals(that.transcriptStartPos) : that.transcriptStartPos != null) + return false; + if (transcriptEndPos != null ? !transcriptEndPos.equals(that.transcriptEndPos) : that.transcriptEndPos != null) return false; if (cDnaChange != null ? !cDnaChange.equals(that.cDnaChange) : that.cDnaChange != null) return false; if (codonChange != null ? !codonChange.equals(that.codonChange) : that.codonChange != null) return false; @@ -435,7 +439,8 @@ public int hashCode() { result = 31 * result + (annotationTranscript != null ? annotationTranscript.hashCode() : 0); result = 31 * result + (transcriptStrand != null ? transcriptStrand.hashCode() : 0); result = 31 * result + (transcriptExon != null ? transcriptExon.hashCode() : 0); - result = 31 * result + (transcriptPos != null ? transcriptPos.hashCode() : 0); + result = 31 * result + (transcriptStartPos != null ? transcriptStartPos.hashCode() : 0); + result = 31 * result + (transcriptEndPos != null ? transcriptEndPos.hashCode() : 0); result = 31 * result + (cDnaChange != null ? cDnaChange.hashCode() : 0); result = 31 * result + (codonChange != null ? codonChange.hashCode() : 0); result = 31 * result + (proteinChange != null ? proteinChange.hashCode() : 0); @@ -474,61 +479,6 @@ public int hashCode() { return result; } - @Override - public String toString() { - return "GencodeFuncotation{" + - "hugoSymbol='" + hugoSymbol + '\'' + - ", ncbiBuild='" + ncbiBuild + '\'' + - ", chromosome='" + chromosome + '\'' + - ", start=" + start + - ", end=" + end + - ", variantClassification=" + variantClassification + - ", secondaryVariantClassification=" + secondaryVariantClassification + - ", variantType=" + variantType + - ", refAllele='" + refAllele + '\'' + - ", tumorSeqAllele2='" + tumorSeqAllele2 + '\'' + - ", genomeChange='" + genomeChange + '\'' + - ", annotationTranscript='" + annotationTranscript + '\'' + - ", transcriptStrand='" + transcriptStrand + '\'' + - ", transcriptExon=" + transcriptExon + - ", transcriptPos=" + transcriptPos + - ", cDnaChange='" + cDnaChange + '\'' + - ", codonChange='" + codonChange + '\'' + - ", proteinChange='" + proteinChange + '\'' + - ", gcContent=" + gcContent + - ", referenceContext='" + referenceContext + '\'' + - ", otherTranscripts=" + otherTranscripts + - ", dataSourceName=" + dataSourceName + - ", locusLevel=" + locusLevel + - ", apprisRank=" + apprisRank + - ", transcriptLength=" + transcriptLength + - ", version='" + version + '\'' + - ", geneTranscriptType=" + geneTranscriptType + - ", hugoSymbolSerializedOverride='" + hugoSymbolSerializedOverride + '\'' + - ", ncbiBuildSerializedOverride='" + ncbiBuildSerializedOverride + '\'' + - ", chromosomeSerializedOverride='" + chromosomeSerializedOverride + '\'' + - ", startSerializedOverride='" + startSerializedOverride + '\'' + - ", endSerializedOverride='" + endSerializedOverride + '\'' + - ", variantClassificationSerializedOverride='" + variantClassificationSerializedOverride + '\'' + - ", secondaryVariantClassificationSerializedOverride='" + secondaryVariantClassificationSerializedOverride + '\'' + - ", variantTypeSerializedOverride='" + variantTypeSerializedOverride + '\'' + - ", refAlleleSerializedOverride='" + refAlleleSerializedOverride + '\'' + - ", tumorSeqAllele1SerializedOverride='" + tumorSeqAllele1SerializedOverride + '\'' + - ", tumorSeqAllele2SerializedOverride='" + tumorSeqAllele2SerializedOverride + '\'' + - ", genomeChangeSerializedOverride='" + genomeChangeSerializedOverride + '\'' + - ", annotationTranscriptSerializedOverride='" + annotationTranscriptSerializedOverride + '\'' + - ", transcriptStrandSerializedOverride='" + transcriptStrandSerializedOverride + '\'' + - ", transcriptExonSerializedOverride='" + transcriptExonSerializedOverride + '\'' + - ", transcriptPosSerializedOverride='" + transcriptPosSerializedOverride + '\'' + - ", cDnaChangeSerializedOverride='" + cDnaChangeSerializedOverride + '\'' + - ", codonChangeSerializedOverride='" + codonChangeSerializedOverride + '\'' + - ", proteinChangeSerializedOverride='" + proteinChangeSerializedOverride + '\'' + - ", gcContentSerializedOverride='" + gcContentSerializedOverride + '\'' + - ", referenceContextSerializedOverride='" + referenceContextSerializedOverride + '\'' + - ", otherTranscriptsSerializedOverride='" + otherTranscriptsSerializedOverride + '\'' + - '}'; - } - //================================================================================================================== public String getHugoSymbol() { @@ -643,12 +593,20 @@ public void setTranscriptExonNumber(final Integer transcriptExonNumber) { this.transcriptExon = transcriptExonNumber; } - public Integer getTranscriptPos() { - return transcriptPos; + public Integer getTranscriptStartPos() { + return transcriptStartPos; + } + + public void setTranscriptStartPos(final Integer transcriptStartPos) { + this.transcriptStartPos = transcriptStartPos; + } + + public Integer getTranscriptEndPos() { + return transcriptEndPos; } - public void setTranscriptPos(final Integer transcriptPos) { - this.transcriptPos = transcriptPos; + public void setTranscriptEndPos(final Integer transcriptEndPos) { + this.transcriptEndPos = transcriptEndPos; } public String getcDnaChange() { @@ -748,35 +706,19 @@ public void setDataSourceName(final String dataSourceName) { public void setMetadata(final FuncotationMetadata metadata) { this.metadata = metadata; } -//================================================================================================================== - /** - * The names of the fields in this GencodeFuncotation. - * Used to access the field map. - */ - private enum FieldName { - hugoSymbol, - ncbiBuild, - chromosome, - start, - end, - variantClassification, - secondaryVariantClassification, - variantType, - refAllele, - tumorSeqAllele1, - tumorSeqAllele2, - genomeChange, - annotationTranscript, - transcriptStrand, - transcriptExon, - transcriptPos, - cDnaChange, - codonChange, - proteinChange, - gcContent, - referenceContext, - otherTranscripts; + //================================================================================================================== + + private String getTranscriptPosString() { + if ( transcriptStartPos == null ) { + return ""; + } + + if ( transcriptStartPos.equals(transcriptEndPos) ) { + return String.valueOf(transcriptStartPos); + } + + return transcriptStartPos + "_" + transcriptEndPos; } //================================================================================================================== diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java index 03257d52023..26da2f9d4c9 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java @@ -160,12 +160,22 @@ public GencodeFuncotationBuilder setAnnotationTranscript(final String transcript } /** - * Set the position (1-based, inclusive) relative to the start of the transcript of a the variant in the {@link GencodeFuncotation}. - * @param transcriptPos The position (1-based, inclusive) relative to the start of the transcript of a the variant in the {@link GencodeFuncotation}. + * Set the start position (1-based, inclusive) relative to the start of the transcript of a the variant in the {@link GencodeFuncotation}. + * @param transcriptStartPos The start position (1-based, inclusive) of the variant in the {@link GencodeFuncotation} relative to the start of the transcript. * @return {@code this} {@link GencodeFuncotationBuilder} */ - public GencodeFuncotationBuilder setTranscriptPos(final Integer transcriptPos) { - gencodeFuncotation.setTranscriptPos(transcriptPos); + public GencodeFuncotationBuilder setTranscriptStartPos(final Integer transcriptStartPos) { + gencodeFuncotation.setTranscriptStartPos(transcriptStartPos); + return this; + } + + /** + * Set the end position (1-based, inclusive) relative to the start of the transcript of a the variant in the {@link GencodeFuncotation}. + * @param transcriptEndPos The end position (1-based, inclusive) of the variant in the {@link GencodeFuncotation} relative to the start of the transcript. + * @return {@code this} {@link GencodeFuncotationBuilder} + */ + public GencodeFuncotationBuilder setTranscriptEndPos(final Integer transcriptEndPos) { + gencodeFuncotation.setTranscriptEndPos(transcriptEndPos); return this; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java index 8637691b093..c689ed3f4b7 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java @@ -795,21 +795,14 @@ private GencodeFuncotation createCodingRegionFuncotationForNonProteinCodingFeatu // Setup the "trivial" fields of the gencodeFuncotation: final GencodeFuncotationBuilder gencodeFuncotationBuilder = createGencodeFuncotationBuilderWithTrivialFieldsPopulated(variant, altAllele, gtfFeature, transcript); - // Set the transcript start position: - gencodeFuncotationBuilder.setTranscriptPos( - FuncotatorUtils.getTranscriptAlleleStartPosition(variant, transcript.getExons(), transcript.getGenomicStrand()) - ); - // Set the exon number: gencodeFuncotationBuilder.setTranscriptExonNumber(exon.getExonNumber()); // Set our version: gencodeFuncotationBuilder.setVersion(version); - // Set our transcript position to be the start point in the transcript of the variant: - gencodeFuncotationBuilder.setTranscriptPos( - FuncotatorUtils.getTranscriptAlleleStartPosition(variant, transcript.getExons(), exon.getGenomicStrand()) - ); + // Set our transcript positions: + setTranscriptPosition(variant, altAllele, transcript, gencodeFuncotationBuilder); // Get the reference bases for our current variant: final StrandCorrectedReferenceBases referenceBases = FuncotatorUtils.createReferenceSnippet(variant.getReference(), altAllele, reference, exon.getGenomicStrand(), referenceWindow); @@ -853,6 +846,48 @@ private GencodeFuncotation createCodingRegionFuncotationForNonProteinCodingFeatu return gencodeFuncotationBuilder.build(); } + /** + * Set the transcript start and end position in the given {@link GencodeFuncotationBuilder}. + * @param variant The {@link VariantContext} for which to set the position. + * @param altAllele The alternate {@link Allele} for which to set the position. + * @param transcript The {@link GencodeGtfTranscriptFeature} in which the {@code variant} occurs. + * @param gencodeFuncotationBuilder The {@link GencodeFuncotationBuilder} in which to set the transcript start and end positions. + */ + private void setTranscriptPosition(final VariantContext variant, final Allele altAllele, final GencodeGtfTranscriptFeature transcript, final GencodeFuncotationBuilder gencodeFuncotationBuilder) { + final int txStart = FuncotatorUtils.getTranscriptAlleleStartPosition(variant, transcript.getExons(), transcript.getGenomicStrand()); + setTranscriptPosition(variant, altAllele, txStart, gencodeFuncotationBuilder); + } + + /** + * Set the transcript start and end position in the given {@link GencodeFuncotationBuilder}. + * @param variant The {@link VariantContext} for which to set the position. + * @param altAllele The alternate {@link Allele} for which to set the position. + * @param txStart The start position of the {@code variant} in the transcript. + * @param gencodeFuncotationBuilder The {@link GencodeFuncotationBuilder} in which to set the transcript start and end positions. + */ + private void setTranscriptPosition(final VariantContext variant, final Allele altAllele, final int txStart, final GencodeFuncotationBuilder gencodeFuncotationBuilder) { + + // Set the transcript start position: + gencodeFuncotationBuilder.setTranscriptStartPos(txStart); + + // For SNPs, start == end: + if ( variant.getReference().length() == 1 ) { + gencodeFuncotationBuilder.setTranscriptEndPos( txStart ); + } + else { + // For indels, we have to adjust by the leading placeholder base. + // For MNPs we can use the raw length. + int indelOffset = 0; + if ( GATKVariantContextUtils.isIndel(variant.getReference(), altAllele) ) { + // Account for the leading base in the variant: + indelOffset = 1; + } + // Subtract 1 here for the inclusive nature of the positions. + // NOTE: this is in addition to the indel offset. + gencodeFuncotationBuilder.setTranscriptEndPos(txStart + variant.getReference().length() - indelOffset -1); + } + } + /** * Create a {@link GencodeFuncotation} for a {@code variant} that occurs in a coding region in a given {@code exon}. * @param variant The {@link VariantContext} for which to create a {@link GencodeFuncotation}. @@ -882,11 +917,6 @@ private GencodeFuncotation createCodingRegionFuncotationForProteinCodingFeature( // Setup the "trivial" fields of the gencodeFuncotation: final GencodeFuncotationBuilder gencodeFuncotationBuilder = createGencodeFuncotationBuilderWithTrivialFieldsPopulated(variant, altAllele, gtfFeature, transcript); - // Set the transcript start position: - gencodeFuncotationBuilder.setTranscriptPos( - FuncotatorUtils.getTranscriptAlleleStartPosition(variant, transcript.getExons(), transcript.getGenomicStrand()) - ); - // Set the exon number: gencodeFuncotationBuilder.setTranscriptExonNumber(exon.getExonNumber()); @@ -897,10 +927,8 @@ private GencodeFuncotation createCodingRegionFuncotationForProteinCodingFeature( // These fields can all be set without knowing the alternate allele: final SequenceComparison sequenceComparison = createSequenceComparison(variant, altAllele, reference, transcript, exonPositionList, transcriptIdMap, transcriptFastaReferenceDataSource, true); - // Set our transcript position to be the start point in the transcript of the variant: - gencodeFuncotationBuilder.setTranscriptPos( - sequenceComparison.getTranscriptAlleleStart() - ); + // Set our transcript positions: + setTranscriptPosition(variant, altAllele, sequenceComparison.getTranscriptAlleleStart(), gencodeFuncotationBuilder); // Set the reference context with the bases from the sequence comparison // NOTE: The reference context is ALWAYS from the + strand, so we need to reverse our bases back in the - case: diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationUnitTest.java index c178711c6e9..1cc44a2940d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationUnitTest.java @@ -27,7 +27,9 @@ private static GencodeFuncotation createGencodeFuncotation(final String hugoSymb final String refAllele, final String tumorSeqAllele2, final String genomeChange, final String annotationTranscript, final String transcriptStrand, - final Integer transcriptExon, final Integer transcriptPos, + final Integer transcriptExon, + final Integer transcriptStartPos, + final Integer transcriptEndPos, final String cDnaChange, final String codonChange, final String proteinChange, final Double gcContent, final String referenceContext, @@ -53,7 +55,8 @@ private static GencodeFuncotation createGencodeFuncotation(final String hugoSymb gencodeFuncotation.setAnnotationTranscript( annotationTranscript ); gencodeFuncotation.setTranscriptStrand( transcriptStrand ); gencodeFuncotation.setTranscriptExonNumber( transcriptExon ); - gencodeFuncotation.setTranscriptPos( transcriptPos ); + gencodeFuncotation.setTranscriptStartPos( transcriptStartPos ); + gencodeFuncotation.setTranscriptEndPos( transcriptEndPos ); gencodeFuncotation.setcDnaChange( cDnaChange ); gencodeFuncotation.setCodonChange( codonChange ); gencodeFuncotation.setProteinChange( proteinChange ); @@ -86,7 +89,7 @@ Object[][] provideForTestGetFieldNames() { createGencodeFuncotation("TESTGENE", "BUILD1", "chr1", 1, 100, GencodeFuncotation.VariantClassification.NONSENSE, GencodeFuncotation.VariantClassification.INTRON, GencodeFuncotation.VariantType.SNP, "A", "T", "big_%20_changes", "T1", - "3'", 1, 1, "A", "ATC", "Lys", 1.0, null, Arrays.asList("ONE", "TWO", "THREE")), + "3'", 1, 1, 1, "A", "ATC", "Lys", 1.0, null, Arrays.asList("ONE", "TWO", "THREE")), new LinkedHashSet<>( Arrays.asList("Gencode_TEST_VERSION_hugoSymbol", "Gencode_TEST_VERSION_ncbiBuild", @@ -122,7 +125,7 @@ Object[][] provideForTestGetField() { final GencodeFuncotation gencodeFuncotation = createGencodeFuncotation("TESTGENE", "BUILD1", "chr1", 1, 100, GencodeFuncotation.VariantClassification.NONSENSE, GencodeFuncotation.VariantClassification.INTRON, GencodeFuncotation.VariantType.SNP, "A", "T", "big_%20_changes", "T1", - "3'", 1, 1, "A", "ATC", "Lys", 1.0, "ATGCGCAT", Arrays.asList("ONE", "TWO", "THREE")); + "3'", 1, 1, 1,"A", "ATC", "Lys", 1.0, "ATGCGCAT", Arrays.asList("ONE", "TWO", "THREE")); return new Object[][] { { @@ -360,7 +363,7 @@ Object[][] provideForTestGetFieldFail() { final GencodeFuncotation gencodeFuncotation = createGencodeFuncotation("TESTGENE", "BUILD1", "chr1", 1, 100, GencodeFuncotation.VariantClassification.NONSENSE, GencodeFuncotation.VariantClassification.INTRON, GencodeFuncotation.VariantType.SNP, "A", "T", "big_%20_changes", "T1", - "3'", 1, 1, "A", "ATC", "Lys", 1.0, "ATGCGCAT", Arrays.asList("ONE", "TWO", "THREE")); + "3'", 1, 1, 1, "A", "ATC", "Lys", 1.0, "ATGCGCAT", Arrays.asList("ONE", "TWO", "THREE")); return new Object[][] { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java index 8c3b56889c1..dde675ca8e2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java @@ -1173,7 +1173,7 @@ private static Funcotation createDummyGencodeFuncotation(final String dummyTrans dummyVariantContext.getReference().getDisplayString(), dummyVariantContext.getAlternateAllele(0).getDisplayString(), "g.1000000"+ dummyVariantContext.getReference().getDisplayString() + ">" + dummyVariantContext.getAlternateAllele(0).getDisplayString(), dummyTranscriptName, Strand.FORWARD, - 1, 1500, + 1, 1500, 1500, " ", " ", "p.L300P", 0.5, "ACTGATCGATCGA",Collections.singletonList("FAKE00002.5"), "27"); diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java b/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java index 766b87ef2f1..93b3069987c 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java @@ -85,7 +85,10 @@ public static FeatureContext createFeatureContext(final List= 1. - * @param transcriptPos 1-based position in the transcript genome sequence. In the Funcotator main code, this field takes into account the coding direction, so it is possible to have + * @param transcriptStartPos 1-based position of the start of the variant in the transcript genome sequence. In the Funcotator main code, this field takes into account the coding direction, so it is possible to have + * a higher transcript position that is a lower position in genomic coordinate space. + * This method will not check validity against the annotation transcript and transcript exon. Must be >= 1. + * @param transcriptEndPos 1-based position of the end of the variant in the transcript genome sequence. In the Funcotator main code, this field takes into account the coding direction, so it is possible to have * a higher transcript position that is a lower position in genomic coordinate space. * This method will not check validity against the annotation transcript and transcript exon. Must be >= 1. * @param cDnaChange This method will not check validity of the specified value. @@ -99,24 +102,27 @@ public static FeatureContext createFeatureContext(final List otherTranscripts, final String version) { + final String chromosome, final int start, final int end, + final GencodeFuncotation.VariantClassification variantClassification, + final GencodeFuncotation.VariantClassification secondaryVariantClassification, + final GencodeFuncotation.VariantType variantType, + final String refAllele, + final String tumorSeqAllele2, final String genomeChange, + final String annotationTranscript, final Strand transcriptStrand, + final Integer transcriptExon, + final Integer transcriptStartPos, + final Integer transcriptEndPos, + final String cDnaChange, final String codonChange, + final String proteinChange, final Double gcContent, + final String referenceContext, + final List otherTranscripts, final String version) { ParamUtils.isPositive(start, "Start position is 1-based and must be greater that zero."); ParamUtils.isPositive(end, "End position is 1-based and must be greater that zero."); ParamUtils.isPositive(transcriptExon, "Transcript exon is a 1-based index."); - ParamUtils.isPositive(transcriptPos, "Transcript position is a 1-based index."); + ParamUtils.isPositive(transcriptStartPos, "Transcript start position is a 1-based index."); + ParamUtils.isPositive(transcriptEndPos, "Transcript end position is a 1-based index."); ParamUtils.inRange(gcContent, 0.0, 1.0, "GC Content must be between 0.0 and 1.0."); final GencodeFuncotationBuilder funcotationBuilder = new GencodeFuncotationBuilder(); @@ -139,7 +145,8 @@ public static GencodeFuncotation createGencodeFuncotation(final String hugoSymbo funcotationBuilder.setAnnotationTranscript( annotationTranscript ); funcotationBuilder.setStrand( transcriptStrand ); funcotationBuilder.setTranscriptExonNumber( transcriptExon ); - funcotationBuilder.setTranscriptPos( transcriptPos ); + funcotationBuilder.setTranscriptStartPos( transcriptStartPos ); + funcotationBuilder.setTranscriptEndPos( transcriptEndPos ); funcotationBuilder.setcDnaChange( cDnaChange ); funcotationBuilder.setCodonChange( codonChange ); funcotationBuilder.setProteinChange( proteinChange ); diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.maf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.maf index 7ab6c2d2f07..4303246d1a9 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.maf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.maf @@ -199,8 +199,8 @@ ## contig= ## contig= ## source=Funcotator -## GATKCommandLine= -## Funcotator 0.0.5 | Date 20184130T024137 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 +## GATKCommandLine= +## Funcotator 0.0.5 | Date 20184831T034835 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_19_secondaryVariantClassification Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_ASSEMBLY ClinVar_rs CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Simple_Uniprot_alt_uniprot_accessions dbSNP_AC dbSNP_AF dbSNP_AN dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DP dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD AC AF ALLELE_A ALLELE_B AN BEADSET_ID FUNCOTATION GC_SCORE ILLUMINA_BUILD ILLUMINA_CHR ILLUMINA_POS ILLUMINA_STRAND N_AA N_AB N_BB PROBE_A PROBE_B SOURCE devR_AA devR_AB devR_BB devTHETA_AA devTHETA_AB devTHETA_BB devX_AA devX_AB devX_BB devY_AA devY_AB devY_BB meanR_AA meanR_AB meanR_BB meanTHETA_AA meanTHETA_AB meanTHETA_BB meanX_AA meanX_AB meanX_BB meanY_AA meanY_AB meanY_BB refSNP zthresh_X zthresh_Y RP11-206L10.10 __UNKNOWN__ hg19 1 752566 752566 + RNA SNP G G A 3094315 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:752566G>A ENST00000435300.1 - c.e1-187C>T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGAGAAACGTTTGACAGAG 0.3690773067331671 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.2817,0.7183 false false 1 false true false FAM87B:400728 true true false true true false false false false false false false false false false true true false true false true false 0 true 0 false 0.351947,0.648053 false false false SNV 0x05012802000515053f000101 1 false 103 rs3094315 752566 true RP11-206L10.10 __UNKNOWN__ hg19 1 752721 752721 + RNA SNP A A G 3131972 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:752721A>G ENST00000435300.1 - c.e1-32T>C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAAGGAAAAGGGAAGAATG 0.486284289276808 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.3466,0.6534 false false 1 false true true FAM87B:400728 true true false true true false false false false false false false false false false false false false true false true false 0 true 0 false 0.393296,0.606704 false false false SNV 0x05010002000517053f000100 1 false 103 rs3131972 752721 true @@ -811,7 +811,7 @@ TNFRSF9 __UNKNOWN__ hg19 1 7999982 7999982 + Nonsense_Mutation SNP G G A __UN PARK7 __UNKNOWN__ hg19 1 8021973 8021973 + 5'UTR SNP G G T 35675666 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8021973G>T ENST00000377491.1 + 1 PARK7_ENST00000493678.1_Intron|PARK7_ENST00000338639.5_Intron|PARK7_ENST00000377493.5_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCGGGGCCTGGGTCGGGGCCG 0.6583541147132169 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8518,.,0.1482 false false 1 false true true PARK7:11315 true true true true true false true false false false false false false false false true true false true false false false 0 true 0 false 0.816402,.,0.183598 false false false SNV 0x0501280a0005170537020100 1 false 126 rs35675666 8021973 true PARK7 __UNKNOWN__ hg19 1 8029464 8029464 + Splice_Site SNP G G A 749774196 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8029464G>A ENST00000493678.1 + 4 319 c.252G>A c.(250-252)gaG>gaA p.E84E PARK7_ENST00000377491.1_Splice_Site_p.E84E|PARK7_ENST00000338639.5_Splice_Site_p.E84E|PARK7_ENST00000377488.1_Splice_Site_p.E84E|PARK7_ENST00000377493.5_Intron|PARK7_ENST00000497113.1_Splice_Site __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATTTATCTGAGGTAAAAAATT 0.3192019950124688 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ SILENT true false false false false false false PARK7:11315 false true true false false false false false false false false false false false false false false false false true false false 0 false 0 true false false false SNV 0x050000080305000402000100 1 false 144 rs749774196 8029464 false PARK7 __UNKNOWN__ hg19 1 8029464 8029464 + Splice_Site SNP G G A 749774196 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8029464G>A ENST00000493678.1 + 4 319 c.252G>A c.(250-252)gaG>gaA p.E84E PARK7_ENST00000377491.1_Splice_Site_p.E84E|PARK7_ENST00000338639.5_Splice_Site_p.E84E|PARK7_ENST00000377488.1_Splice_Site_p.E84E|PARK7_ENST00000377493.5_Intron|PARK7_ENST00000497113.1_Splice_Site __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATTTATCTGAGGTAAAAAATT 0.3192019950124688 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ SILENT true false false false false false false PARK7:11315 false true true false false false false false false false false false false false false false false false false true false false 0 false 0 true false false false SNV 0x050000080305000402000100 1 false 144 rs749774196 8029464 false -PARK7 __UNKNOWN__ hg19 1 8045015 8045020 + In_Frame_Del DEL GCC GCC - 764877312 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8045015_8045017delGCC ENST00000493678.1 + 7 537 c.471_473delGCC c.(469-474)gggcct>ggt p.P158del PARK7_ENST00000377491.1_In_Frame_Del_p.P158del|PARK7_ENST00000338639.5_In_Frame_Del_p.P158del|PARK7_ENST00000377488.1_In_Frame_Del_p.P158del|PARK7_ENST00000377493.5_In_Frame_Del_p.P138del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGCCGGGGGCCTGGGACCAGC 0.4466501240694789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PARK7:11315 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005040402000200 1 false 144 rs764877312 8045015 true +PARK7 __UNKNOWN__ hg19 1 8045015 8045020 + In_Frame_Del DEL GCC GCC - 764877312 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8045015_8045017delGCC ENST00000493678.1 + 7 537_539 c.471_473delGCC c.(469-474)gggcct>ggt p.P158del PARK7_ENST00000377491.1_In_Frame_Del_p.P158del|PARK7_ENST00000338639.5_In_Frame_Del_p.P158del|PARK7_ENST00000377488.1_In_Frame_Del_p.P158del|PARK7_ENST00000377493.5_In_Frame_Del_p.P138del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGCCGGGGGCCTGGGACCAGC 0.4466501240694789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PARK7:11315 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005040402000200 1 false 144 rs764877312 8045015 true ERRFI1 __UNKNOWN__ hg19 1 8073830 8073830 + 3'UTR SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8073830C>T ENST00000469499.1 - 3 ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000377482.5_Missense_Mutation_p.D277N|ERRFI1_ENST00000467067.1_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTGTCTTCATCGGAGTTAGGA 0.48877805486284287 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ERRFI1 __UNKNOWN__ hg19 1 8073919 8073919 + 3'UTR SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8073919C>T ENST00000469499.1 - 3 ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000377482.5_Missense_Mutation_p.R247K|ERRFI1_ENST00000467067.1_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATGAGACCTTCTTAATCTTCG 0.46384039900249374 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ERRFI1 __UNKNOWN__ hg19 1 8073925 8073925 + 3'UTR SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8073925C>T ENST00000469499.1 - 3 ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000377482.5_Missense_Mutation_p.R245K|ERRFI1_ENST00000467067.1_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTTCTTAATCTTCGGTGGGT 0.46384039900249374 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -916,7 +916,7 @@ CLCN6 __UNKNOWN__ hg19 1 11901592 11901592 + 3'UTR SNP T T C 198415 byFrequency NPPA __UNKNOWN__ hg19 1 11906068 11906068 + Nonstop_Mutation SNP A A G 5065 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:11906068A>G ENST00000376480.3 - 3 553 c.454T>C c.(454-456)Tga>Cga p.*152R NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA-AS1_ENST00000446542.1_RNA|NPPA-AS1_ENST00000400892.2_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGTTATCTTCAGTACTGCAAA 0.4937655860349127 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8209,0.1791 false false 1 false true false NPPA:4878|NPPA-AS1:100379251 true true true true true false false false false false false false false false false true true false false true false false 0 true 0 false 0.737688,0.262312 true false false SNV 0x05013808020515053f000100 1 false 52 rs5065 11906068 true NPPA __UNKNOWN__ hg19 1 11906068 11906068 + Nonstop_Mutation SNP A A G 5065 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:11906068A>G ENST00000376480.3 - 3 553 c.454T>C c.(454-456)Tga>Cga p.*152R NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA-AS1_ENST00000446542.1_RNA|NPPA-AS1_ENST00000400892.2_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGTTATCTTCAGTACTGCAAA 0.4937655860349127 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8209,0.1791 false false 1 false true false NPPA:4878|NPPA-AS1:100379251 true true true true true false false false false false false false false false false true true false false true false false 0 true 0 false 0.737688,0.262312 true false false SNV 0x05013808020515053f000100 1 false 52 rs5065 11906068 true PLOD1 __UNKNOWN__ hg19 1 12025599 12025599 + Nonsense_Mutation SNP C C G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12025599C>G ENST00000196061.4 + 14 1560 c.1533C>G c.(1531-1533)taC>taG p.Y511* PLOD1_ENST00000376369.3_Nonsense_Mutation_p.Y558* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TAGACAGCTACCGCACCACCC 0.6384039900249376 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -MFN2 __UNKNOWN__ hg19 1 12069757 12069764 + Frame_Shift_Del DEL ACTT ACTT - 772270096 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12069757_12069760delACTT ENST00000235329.5 + 18 2499 c.2178_2181delACTT c.(2176-2181)tcacttfs p.L727fs MFN2_ENST00000444836.1_Frame_Shift_Del_p.L727fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCTTGACTCACTTCAGAGCAAAG 0.5693069306930693 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false MFN2:9927 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs772270096 12069757 false +MFN2 __UNKNOWN__ hg19 1 12069757 12069764 + Frame_Shift_Del DEL ACTT ACTT - 772270096 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12069757_12069760delACTT ENST00000235329.5 + 18 2499_2502 c.2178_2181delACTT c.(2176-2181)tcacttfs p.L727fs MFN2_ENST00000444836.1_Frame_Shift_Del_p.L727fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCTTGACTCACTTCAGAGCAAAG 0.5693069306930693 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false MFN2:9927 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs772270096 12069757 false MIIP __UNKNOWN__ hg19 1 12082195 12082195 + Nonsense_Mutation SNP C C A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12082195C>A ENST00000235332.4 + 3 327 c.158C>A c.(157-159)tCg>tAg p.S53* MIIP_ENST00000436478.2_Nonsense_Mutation_p.S53* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGACTCCATCGACCCCAGAG 0.6483790523690773 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MIIP __UNKNOWN__ hg19 1 12090140 12090140 + Nonsense_Mutation SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12090140C>T ENST00000235332.4 + 8 1070 c.901C>T c.(901-903)Cga>Tga p.R301* MIIP_ENST00000436478.2_Intron|MIIP_ENST00000466860.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CATCCACCGGCGAAAGAGCTT 0.6533665835411472 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false VPS13D __UNKNOWN__ hg19 1 12318010 12318010 + Nonsense_Mutation SNP T T G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12318010T>G ENST00000358136.3 + 10 1090 c.960T>G c.(958-960)taT>taG p.Y320* VPS13D_ENST00000356315.4_Nonsense_Mutation_p.Y320* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AATGGTGGTATTTTGCTTTGA 0.4164588528678304 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1080,7 +1080,7 @@ PINK1 __UNKNOWN__ hg19 1 20976995 20976996 + Frame_Shift_Del DEL G G - __UNKN PINK1-AS __UNKNOWN__ hg19 1 20978058 20978058 + RNA SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20978058G>A ENST00000451424.1 - c.e1-628C>T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCATTTCAGTGATTCCCACCC 0.4239401496259352 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PINK1-AS __UNKNOWN__ hg19 1 20978058 20978058 + RNA SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20978058G>A ENST00000451424.1 - c.e1-628C>T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCATTTCAGTGATTCCCACCC 0.4239401496259352 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false DDOST __UNKNOWN__ hg19 1 20987879 20987879 + 5'UTR SNP A A C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20987879A>C ENST00000602624.2 - 1 DDOST_ENST00000375048.3_Missense_Mutation_p.C6G|DDOST_ENST00000415136.2_Missense_Mutation_p.C6G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCACGTGCACACCGGAAGTAC 0.6508728179551122 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -KIF17 __UNKNOWN__ hg19 1 20998553 20998556 + Frame_Shift_Del DEL AG AG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20998553_20998554delAG ENST00000247986.2 - 12 2912 c.2599_2600delCT c.(2599-2601)ctgfs p.L867fs KIF17_ENST00000400463.3_Frame_Shift_Del_p.L867fs|KIF17_ENST00000375044.1_Frame_Shift_Del_p.L767fs|KIF17_ENST00000490034.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTGCGAATCAGGGGCTGCACC 0.5696517412935324 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +KIF17 __UNKNOWN__ hg19 1 20998553 20998556 + Frame_Shift_Del DEL AG AG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20998553_20998554delAG ENST00000247986.2 - 12 2912_2913 c.2599_2600delCT c.(2599-2601)ctgfs p.L867fs KIF17_ENST00000400463.3_Frame_Shift_Del_p.L867fs|KIF17_ENST00000375044.1_Frame_Shift_Del_p.L767fs|KIF17_ENST00000490034.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTGCGAATCAGGGGCTGCACC 0.5696517412935324 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false SH2D5 __UNKNOWN__ hg19 1 21047725 21047725 + 3'UTR SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:21047725A>G ENST00000375031.1 - 9 SH2D5_ENST00000460804.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCAGATACATATGAGAAACAG 0.5810473815461347 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ECE1 __UNKNOWN__ hg19 1 21544601 21544601 + 3'UTR SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:21544601C>T ENST00000415912.2 - 19 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGTCTGCTACTGGAGAAGCT 0.6184538653366584 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false RP11-293F5.1 __UNKNOWN__ hg19 1 21742614 21742614 + RNA SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:21742614T>C ENST00000444647.1 + c.e1+186T>C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCCTGAGAGATCCCAACAGTC 0.5311720698254364 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1122,7 +1122,7 @@ RP11-70P17.1 __UNKNOWN__ hg19 1 25908805 25908805 + RNA SNP T T C __UNKNOWN__ RP11-70P17.1 __UNKNOWN__ hg19 1 25914219 25914219 + RNA SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:25914219T>C ENST00000412797.1 + c.e2-2441T>C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAAGAGTTACTGAGAACTGCT 0.48877805486284287 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false AUNIP __UNKNOWN__ hg19 1 26161572 26161573 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26161572delT ENST00000374298.3 - 3 1042 c.986delA c.(985-987)cagfs p.Q329fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.Q329fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCCATCCTCCTGGCACTGAGC 0.44139650872817954 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false AUNIP __UNKNOWN__ hg19 1 26161630 26161631 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26161630delT ENST00000374298.3 - 3 984 c.928delA c.(928-930)accfs p.T310fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.T310fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAGTTATTGGTTACATCTTGA 0.4339152119700748 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -AUNIP __UNKNOWN__ hg19 1 26161799 26161802 + Frame_Shift_Del DEL GG GG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26161799_26161800delGG ENST00000374298.3 - 3 815 c.758_759delCC c.(757-762)tcctggfs p.S253fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.S253fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTCCATTCCAGGATTCCCTGTA 0.4527363184079602 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +AUNIP __UNKNOWN__ hg19 1 26161799 26161802 + Frame_Shift_Del DEL GG GG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26161799_26161800delGG ENST00000374298.3 - 3 815_816 c.758_759delCC c.(757-762)tcctggfs p.S253fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.S253fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTCCATTCCAGGATTCCCTGTA 0.4527363184079602 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false AUNIP __UNKNOWN__ hg19 1 26161916 26161917 + Frame_Shift_Del DEL G G - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26161916delG ENST00000374298.3 - 3 698 c.642delC c.(640-642)cacfs p.H214fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.H214fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTAGTTTGGTGTGTTTCTCCA 0.4488778054862843 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false AUNIP __UNKNOWN__ hg19 1 26164009 26164010 + Frame_Shift_Del DEL G G - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26164009delG ENST00000374298.3 - 2 171 c.115delC c.(115-117)ctcfs p.L39fs AUNIP_ENST00000538789.1_Frame_Shift_Del_p.L39fs|AUNIP_ENST00000481602.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCAGGAAGGAGTGTTAGCATT 0.39650872817955113 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PAFAH2 __UNKNOWN__ hg19 1 26301007 26301008 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26301007delC ENST00000374282.3 - 9 1074 c.893delG c.(892-894)tgtfs p.C298fs PAFAH2_ENST00000374284.1_Frame_Shift_Del_p.C298fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATGCTGGGCACATATCTTCTT 0.4538653366583541 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1185,21 +1185,21 @@ CCDC30 __UNKNOWN__ hg19 1 43004895 43004896 + Frame_Shift_Del DEL A A - __UNK CCDC30 __UNKNOWN__ hg19 1 43021828 43021829 + Splice_Site DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43021828delC ENST00000340612.4 + 4 426 c.427delC c.(427-429)cccfs p.K144fs CCDC30_ENST00000507855.1_Intron|CCDC30_ENST00000428554.2_Splice_Site_p.K144fs|CCDC30_ENST00000342022.4_Splice_Site_p.K144fs|CCDC30_ENST00000390640.4_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGCACCAAGTCCCAAATTAGG 0.38902743142144636 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ FRAME_SHIFT_DEL false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false C1orf50 __UNKNOWN__ hg19 1 43232984 43232984 + START_CODON_SNP SNP T T C 200116115 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43232984T>C ENST00000372525.5 + 1 45 c.2T>C c.(1-3)aTg>aCg p.M1T C1orf50_ENST00000536543.1_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGCGCTGTCATGGAGGACGCC 0.6957605985037406 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.9996,.,0.0003994 false false 0 false false false P3H1:64175|C1orf50:79078 false true false true true false false false false false false true false false false false false false true true false false 0 false 0 false 0.999622,0.000171715,0.000206058 false false false SNV 0x050000020a05040436000100 1 false 137 rs200116115 43232984 true FAM183A __UNKNOWN__ hg19 1 43610910 43610910 + 5'UTR SNP T T G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43610910T>G ENST00000410048.1 + 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGCAGGGCCATTGACAGAGAA 0.47880299251870323 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -TIE1 __UNKNOWN__ hg19 1 43783610 43783617 + Frame_Shift_Del DEL GGAA GGAA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43783610_43783613delGGAA ENST00000372476.3 + 17 2867 c.2789_2792delGGAA c.(2788-2793)cggaaafs p.R930fs TIE1_ENST00000433781.2_Frame_Shift_Del_p.R575fs|TIE1_ENST00000473014.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GATTTTCTGCGGAAAAGCCGGGTC 0.5668316831683168 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +TIE1 __UNKNOWN__ hg19 1 43783610 43783617 + Frame_Shift_Del DEL GGAA GGAA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43783610_43783613delGGAA ENST00000372476.3 + 17 2867_2870 c.2789_2792delGGAA c.(2788-2793)cggaaafs p.R930fs TIE1_ENST00000433781.2_Frame_Shift_Del_p.R575fs|TIE1_ENST00000473014.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GATTTTCTGCGGAAAAGCCGGGTC 0.5668316831683168 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MED8 __UNKNOWN__ hg19 1 43854091 43854091 + 5'UTR SNP C C G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:43854091C>G ENST00000372455.4 - 2 MED8_ENST00000372457.4_Missense_Mutation_p.E5D|MED8_ENST00000290663.6_Missense_Mutation_p.E5D|RP1-92O14.6_ENST00000436713.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGCTGCTTCTCCTCTCTCT 0.4837905236907731 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false B4GALT2 __UNKNOWN__ hg19 1 44445667 44445667 + 5'UTR SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:44445667T>C ENST00000356836.6 + 1 B4GALT2_ENST00000372324.1_Intron|B4GALT2_ENST00000434555.2_Intron|B4GALT2_ENST00000309519.7_5'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 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false false false false UROD __UNKNOWN__ hg19 1 45477940 45477940 + START_CODON_SNP SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:45477940G>A ENST00000246337.4 + 1 122 c.3G>A c.(1-3)atG>atA p.M1I UROD_ENST00000494399.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGCTGACCATGGAAGCGAATG 0.543640897755611 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -CCDC163P __UNKNOWN__ hg19 1 45965247 45965262 + Frame_Shift_Del DEL TCCAGCTG TCCAGCTG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:45965247_45965254delTCCAGCTG ENST00000432082.1 - 1 401 c.28_35delCAGCTGGA c.(28-36)cagctggatfs p.Q10fs CCDC163P_ENST00000488405.2_Frame_Shift_Del_p.Q10fs|CCDC163P_ENST00000490551.3_Frame_Shift_Del_p.Q10fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGCACATCCAGCTGCTCAAACCAG 0.5465686274509803 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +CCDC163P __UNKNOWN__ hg19 1 45965247 45965262 + Frame_Shift_Del DEL TCCAGCTG TCCAGCTG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:45965247_45965254delTCCAGCTG ENST00000432082.1 - 1 401_408 c.28_35delCAGCTGGA c.(28-36)cagctggatfs p.Q10fs CCDC163P_ENST00000488405.2_Frame_Shift_Del_p.Q10fs|CCDC163P_ENST00000490551.3_Frame_Shift_Del_p.Q10fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGCACATCCAGCTGCTCAAACCAG 0.5465686274509803 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MMACHC __UNKNOWN__ hg19 1 45974886 45974886 + Nonstop_Mutation SNP G G C 201025783 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:45974886G>C ENST00000401061.4 + 4 1128 c.848G>C c.(847-849)tGa>tCa p.*283S __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTGGCCCTTGATTTTCTCCC 0.5112219451371571 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false MMACHC:25974 false true false true false false false false false false false false false false false false false false false true false false 0 false 0 false 0.999244,0.000240401,0.000515145 false false false SNV 0x050000000205040416000100 1 false 137 rs201025783 45974886 true AKR1A1 __UNKNOWN__ hg19 1 46032296 46032297 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46032296delC ENST00000372070.3 + 4 886 c.140delC c.(139-141)gctfs p.A47fs AKR1A1_ENST00000351829.4_Frame_Shift_Del_p.A47fs|AKR1A1_ENST00000471651.1_Frame_Shift_Del_p.A47fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATTGATTGTGCTGCTATCTAC 0.5261845386533666 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -CCDC17 __UNKNOWN__ hg19 1 46086466 46086469 + Frame_Shift_Del DEL TT TT - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46086466_46086467delTT ENST00000528266.1 - 12 1788 c.1638_1639delAA c.(1636-1638)gcafs p.D548fs CCDC17_ENST00000421127.2_Frame_Shift_Del_p.D539fs|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000343901.2_Frame_Shift_Del_p.D516fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTGCATCTCTTGCATTCACCA 0.5597014925373134 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +CCDC17 __UNKNOWN__ hg19 1 46086466 46086469 + Frame_Shift_Del DEL TT TT - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46086466_46086467delTT ENST00000528266.1 - 12 1788_1789 c.1638_1639delAA c.(1636-1638)gcafs p.D548fs CCDC17_ENST00000421127.2_Frame_Shift_Del_p.D539fs|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000343901.2_Frame_Shift_Del_p.D516fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTGCATCTCTTGCATTCACCA 0.5597014925373134 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false CCDC17 __UNKNOWN__ hg19 1 46087134 46087135 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46087134delC ENST00000528266.1 - 10 1356 c.1207delG c.(1207-1209)gatfs p.D403fs CCDC17_ENST00000421127.2_Frame_Shift_Del_p.D394fs|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000343901.2_Frame_Shift_Del_p.D371fs|CCDC17_ENST00000464739.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGCAGGAAATCATAGAAAATG 0.600997506234414 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false GPBP1L1 __UNKNOWN__ hg19 1 46120884 46120885 + Frame_Shift_Del DEL A A - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46120884delA ENST00000290795.3 - 4 1391 c.168delT c.(166-168)aatfs p.N56fs GPBP1L1_ENST00000355105.3_Frame_Shift_Del_p.N56fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTAGGGGACCATTGTTAAAAA 0.4014962593516209 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false GPBP1L1 __UNKNOWN__ hg19 1 46125880 46125880 + 5'UTR SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46125880T>C ENST00000290795.3 - 2 GPBP1L1_ENST00000355105.3_5'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTGTGGTCCTGTTTCTGAAC 0.428927680798005 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TMEM69 __UNKNOWN__ hg19 1 46153203 46153203 + 5'UTR SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46153203G>A ENST00000372025.4 + 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACACGGAAGGGCACTAAAATT 0.5012468827930174 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -TMEM69 __UNKNOWN__ hg19 1 46158965 46158968 + Frame_Shift_Del DEL AT AT - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46158965_46158966delAT ENST00000372025.4 + 3 1288 c.132_133delAT c.(130-135)ccatgtfs p.C45fs TMEM69_ENST00000496366.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACTTTTCCCCATGTCCAAGGCC 0.4129353233830846 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +TMEM69 __UNKNOWN__ hg19 1 46158965 46158968 + Frame_Shift_Del DEL AT AT - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46158965_46158966delAT ENST00000372025.4 + 3 1288_1289 c.132_133delAT c.(130-135)ccatgtfs p.C45fs TMEM69_ENST00000496366.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACTTTTCCCCATGTCCAAGGCC 0.4129353233830846 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TMEM69 __UNKNOWN__ hg19 1 46159032 46159033 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46159032delT ENST00000372025.4 + 3 1355 c.199delT c.(199-201)tccfs p.S67fs TMEM69_ENST00000496366.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTATCATACATCCCCCTGCAG 0.42144638403990026 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3R3 __UNKNOWN__ hg19 1 46543211 46543212 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46543211delT ENST00000262741.5 - 3 981 c.290delA c.(289-291)cagfs p.Q97fs PIK3R3_ENST00000420542.1_Frame_Shift_Del_p.Q97fs|PIK3R3_ENST00000372006.1_Frame_Shift_Del_p.Q97fs|PIK3R3_ENST00000423209.1_Frame_Shift_Del_p.Q97fs|PIK3R3_ENST00000354242.4_Frame_Shift_Del_p.Q97fs|PIK3R3_ENST00000340332.6_Frame_Shift_Del_p.Q61fs|PIK3R3_ENST00000540385.1_Frame_Shift_Del_p.Q143fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATAATCTCCCTGCATTTTTGT 0.3516209476309227 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3R3 __UNKNOWN__ hg19 1 46598273 46598273 + 5'UTR SNP A A C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:46598273A>C ENST00000262741.5 - 1 PIK3R3_ENST00000420542.1_Intron|PIK3R3_ENST00000372006.1_Intron|PIK3R3_ENST00000423209.1_5'UTR|PIK3R3_ENST00000354242.4_Intron|PIK3R3_ENST00000340332.6_Intron|PIK3R3_ENST00000540385.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AACCAACCCGACCGCACCAAC 0.6708229426433915 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1229,7 +1229,7 @@ RP11-567C20.3 __UNKNOWN__ hg19 1 50679059 50679059 + RNA SNP G G A __UNKNOWN_ TTC39A __UNKNOWN__ hg19 1 51770774 51770775 + Frame_Shift_Del DEL A A - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:51770774delA ENST00000262676.5 - 8 891 c.729delT c.(727-729)tttfs p.F243fs TTC39A_ENST00000447632.2_Frame_Shift_Del_p.F247fs|TTC39A_ENST00000413473.2_Frame_Shift_Del_p.F215fs|TTC39A_ENST00000262675.7_Frame_Shift_Del_p.F184fs|TTC39A_ENST00000371750.5_Frame_Shift_Del_p.F212fs|TTC39A_ENST00000371747.3_Frame_Shift_Del_p.F246fs|TTC39A_ENST00000451380.1_Frame_Shift_Del_p.F211fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAAACCCCACAAACTCCAACA 0.57356608478803 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TXNDC12 __UNKNOWN__ hg19 1 52521798 52521798 + 5'UTR SNP G G T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:52521798G>T ENST00000371626.4 - 1 BTF3L4_ENST00000313334.8_5'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGACTGCAAGCCCCAGGATG 0.5586034912718204 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ORC1 __UNKNOWN__ hg19 1 52859336 52859337 + Frame_Shift_Del DEL A A - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:52859336delA ENST00000371568.3 - 6 1081 c.861delT c.(859-861)tctfs p.P288fs ORC1_ENST00000371566.1_Frame_Shift_Del_p.P288fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCAGAGCTGGAGACAAGGTTT 0.4463840399002494 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -SELRC1 __UNKNOWN__ hg19 1 53158511 53158538 + Frame_Shift_Del DEL TTCCAAATAGTCCA TTCCAAATAGTCCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:53158511_53158524delTTCCAAATAGTCCA ENST00000371538.3 - 2 176 c.122_135delTGGACTATTTGGAA c.(121-138)gtggactatttggaagggfs p.V41fs SELRC1_ENST00000486918.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCGGATCCCTTCCAAATAGTCCACCAGCCGATA 0.5289855072463768 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +SELRC1 __UNKNOWN__ hg19 1 53158511 53158538 + Frame_Shift_Del DEL TTCCAAATAGTCCA TTCCAAATAGTCCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:53158511_53158524delTTCCAAATAGTCCA ENST00000371538.3 - 2 176_189 c.122_135delTGGACTATTTGGAA c.(121-138)gtggactatttggaagggfs p.V41fs SELRC1_ENST00000486918.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCGGATCCCTTCCAAATAGTCCACCAGCCGATA 0.5289855072463768 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false SELRC1 __UNKNOWN__ hg19 1 53163902 53163903 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:53163902delC ENST00000371538.3 - 1 138 c.97delG c.(97-99)gacfs p.D33fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCGTCCGGGTCCTTCTCGTGG 0.6982543640897756 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false LRP8 __UNKNOWN__ hg19 1 53741391 53741391 + 5'UTR SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:53741391A>G ENST00000465675.1 - 5 LRP8_ENST00000347547.2_Intron|LRP8_ENST00000306052.6_Silent_p.C306C|LRP8_ENST00000371454.2_Silent_p.C306C|LRP8_ENST00000354412.3_Silent_p.C177C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCCATCCCCACACTGGAACT 0.57356608478803 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false YIPF1 __UNKNOWN__ hg19 1 54354613 54354613 + 5'UTR SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:54354613G>A ENST00000072644.1 - 3 YIPF1_ENST00000371399.1_Intron|YIPF1_ENST00000539954.1_Nonsense_Mutation_p.R25*|YIPF1_ENST00000469457.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTGCCATTCGGCCAGTGAGT 0.38403990024937656 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1243,7 +1243,7 @@ C1orf177 __UNKNOWN__ hg19 1 55273583 55273584 + Frame_Shift_Del DEL T T - 76123 C1orf177 __UNKNOWN__ hg19 1 55307524 55307525 + Frame_Shift_Del DEL A A - 777519771 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:55307524delA ENST00000371273.3 + 10 1249 c.1235delA c.(1234-1236)tacfs p.Y412fs C1orf177_ENST00000358193.3_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACTGTGGATTACAATTCAGAT 0.4937655860349127 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false LEXM:163747 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false true false DIV 0x050000801205000402000200 1 false 144 rs777519771 55307524 false C1orf168 __UNKNOWN__ hg19 1 57258131 57258132 + Frame_Shift_Del DEL G G - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:57258131delG ENST00000343433.6 - 2 437 c.355delC c.(355-357)caafs p.Q119fs C1orf168_ENST00000484327.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACATTTGATTGAGTCACCTCT 0.456359102244389 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false C8A __UNKNOWN__ hg19 1 57351823 57351824 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:57351823delC 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g.chr1:63902554_63902555delCC ENST00000263440.4 + 14 1600_1601 c.1393_1394delCC c.(1393-1395)cctfs p.P465fs ALG6_ENST00000371108.4_Frame_Shift_Del_p.P463fs|ALG6_ENST00000494765.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACTGGATCCTCCTCAGAAACTA 0.35572139303482586 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +EFCAB7 __UNKNOWN__ hg19 1 63999794 63999797 + Frame_Shift_Del DEL AA AA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:63999794_63999795delAA ENST00000371088.4 + 6 956_957 c.711_712delAA c.(709-714)gcaaccfs 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ENST00000354777.2 - 12 1820 c.1573delG c.(1573-1575)gaafs p.E525fs WLS_ENST00000540432.1_Frame_Shift_Del_p.E527fs|GNG12-AS1_ENST00000420587.1_RNA|GNG12-AS1_ENST00000413628.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAACAATTCTTGATAAAGT 0.3341645885286783 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false WLS __UNKNOWN__ hg19 1 68564393 68564394 + Frame_Shift_Del DEL A A - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:68564393delA ENST00000354777.2 - 12 1801 c.1554delT c.(1552-1554)tttfs p.F518fs 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p.T355fs CTH_ENST00000346806.2_Frame_Shift_Del_p.T311fs|CTH_ENST00000411986.2_Frame_Shift_Del_p.T323fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCAATCATGACTCATGCATCA 0.38902743142144636 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PTGER3 __UNKNOWN__ hg19 1 71418632 71418633 + Frame_Shift_Del DEL G G - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:71418632delG ENST00000356595.4 - 4 1427 c.1215delC c.(1213-1215)agcfs p.S405fs PTGER3_ENST00000414819.1_3'UTR|PTGER3_ENST00000370931.3_Intron|PTGER3_ENST00000460330.1_Intron|PTGER3_ENST00000370932.2_Intron|PTGER3_ENST00000351052.5_Intron|PTGER3_ENST00000354608.5_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACACATTAATGCTGCTCACGA 0.3740648379052369 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false LRRIQ3 __UNKNOWN__ hg19 1 74663709 74663709 + 5'UTR SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:74663709G>A ENST00000370911.3 - 1 LRRIQ3_ENST00000370909.2_5'UTR|LRRIQ3_ENST00000354431.4_5'UTR 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TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.G124fs|FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.G238fs|FPGT-TNNI3K_ENST00000370895.1_Frame_Shift_Del_p.G225fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.G225fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTTCACAGTGGAGCTGATATACAG 0.3950617283950617 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false TNNI3K:51086|FPGT-TNNI3K:100526835 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs761357894 74737318 false -FPGT-TNNI3K __UNKNOWN__ hg19 1 74835231 74835234 + Frame_Shift_Del DEL AG AG - 748927643 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:74835231_74835232delAG ENST00000370899.3 + 18 1968 c.1932_1933delAG c.(1930-1935)tcagggfs p.G646fs TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.G545fs|FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.G659fs|FPGT-TNNI3K_ENST00000370895.1_Frame_Shift_Del_p.G646fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.G646fs|RP11-439H8.4_ENST00000415549.2_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AATACATATCAGGGGGTTCTCT 0.43034825870646765 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false TNNI3K:51086|FPGT-TNNI3K:100526835 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs748927643 74835231 false +FPGT-TNNI3K __UNKNOWN__ hg19 1 74737318 74737327 + Frame_Shift_Del DEL GGAGC GGAGC - 761357894 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:74737318_74737322delGGAGC ENST00000370899.3 + 7 709_713 c.673_677delGGAGC c.(673-678)ggagctfs p.G225fs TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.G124fs|FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.G238fs|FPGT-TNNI3K_ENST00000370895.1_Frame_Shift_Del_p.G225fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.G225fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTTCACAGTGGAGCTGATATACAG 0.3950617283950617 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false TNNI3K:51086|FPGT-TNNI3K:100526835 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs761357894 74737318 false +FPGT-TNNI3K __UNKNOWN__ hg19 1 74835231 74835234 + Frame_Shift_Del DEL AG AG - 748927643 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:74835231_74835232delAG ENST00000370899.3 + 18 1968_1969 c.1932_1933delAG c.(1930-1935)tcagggfs p.G646fs TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.G545fs|FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.G659fs|FPGT-TNNI3K_ENST00000370895.1_Frame_Shift_Del_p.G646fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.G646fs|RP11-439H8.4_ENST00000415549.2_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AATACATATCAGGGGGTTCTCT 0.43034825870646765 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false TNNI3K:51086|FPGT-TNNI3K:100526835 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs748927643 74835231 false C1orf173 __UNKNOWN__ hg19 1 75036873 75036874 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:75036873delT ENST00000326665.5 - 14 4741 c.4521delA c.(4519-4521)cgafs p.E1508fs C1orf173_ENST00000433746.2_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTTGCTTCTCTCGGGTTTCAG 0.5336658354114713 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false C1orf173 __UNKNOWN__ hg19 1 75038573 75038574 + Frame_Shift_Del DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:75038573delC ENST00000326665.5 - 14 3041 c.2821delG c.(2821-2823)gatfs p.D941fs C1orf173_ENST00000433746.2_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTCCGACATCACTCACAGCC 0.5336658354114713 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false CRYZ __UNKNOWN__ hg19 1 75198740 75198740 + 5'UTR SNP A A C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:75198740A>C ENST00000417775.1 - 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCACCCAGGATGTGCGCCTC 0.5311720698254364 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1400,7 +1400,7 @@ LIPA __UNKNOWN__ hg19 10 90988034 90988035 + Frame_Shift_Ins INS - - GG __UNK MYOF __UNKNOWN__ hg19 10 95121241 95121242 + Frame_Shift_Ins INS - - GT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:95121241_95121242insGT ENST00000359263.4 - 28 2942 c.2941_2942insAC c.(2941-2943)tctfs p.S981fs MYOF_ENST00000358334.5_Frame_Shift_Ins_p.S968fs|MYOF_ENST00000371501.4_Frame_Shift_Ins_p.S981fs|MYOF_ENST00000371502.4_Frame_Shift_Ins_p.S981fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATGTCATAAGACCATGCATC 0.47 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PKD2L1 __UNKNOWN__ hg19 10 102048159 102048160 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:102048159_102048160insA ENST00000318222.3 - 16 2795 c.2411_2412insT c.(2410-2412)aggfs p.R804fs PKD2L1_ENST00000338519.3_Frame_Shift_Ins_p.R729fs|PKD2L1_ENST00000353274.3_3'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CACTTAACTCCTCTGCAACG 0.465 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false FAM178A __UNKNOWN__ hg19 10 102684419 102684420 + Frame_Shift_Ins INS - - T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:102684419_102684420insT ENST00000238961.4 + 5 2203 c.1661_1662insT c.(1660-1662)aagfs p.K554fs FAM178A_ENST00000370269.3_Frame_Shift_Ins_p.K554fs|FAM178A_ENST00000370271.3_Frame_Shift_Ins_p.K554fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTCCTACAAAGTCTCCCCCT 0.4225 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -EIF3A __UNKNOWN__ hg19 10 120795682 120795705 + In_Frame_Del DEL CTCGGTCTCTTG CTCGGTCTCTTG - 766037789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:120795682_120795693delCTCGGTCTCTTG ENST00000369144.3 - 22 4147 c.4007_4018delCAAGAGACCGAG c.(4006-4020)tcaagagaccgagaa>taa p.1336_1340SRDRE>* EIF3A_ENST00000541549.1_In_Frame_Del_p.1302_1306SRDRE>* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG 0.3859223300970874 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false EIF3A:8661 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005000402000200 1 false 144 rs766037789 120795682 false +EIF3A __UNKNOWN__ hg19 10 120795682 120795705 + In_Frame_Del DEL CTCGGTCTCTTG CTCGGTCTCTTG - 766037789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:120795682_120795693delCTCGGTCTCTTG ENST00000369144.3 - 22 4147_4158 c.4007_4018delCAAGAGACCGAG c.(4006-4020)tcaagagaccgagaa>taa p.1336_1340SRDRE>* EIF3A_ENST00000541549.1_In_Frame_Del_p.1302_1306SRDRE>* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG 0.3859223300970874 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false EIF3A:8661 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005000402000200 1 false 144 rs766037789 120795682 false INPP5F __UNKNOWN__ hg19 10 121541194 121541195 + Frame_Shift_Ins INS - - G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:121541194_121541195insG ENST00000361976.2 + 3 392 c.226_227insG c.(226-228)aaafs p.K76fs INPP5F_ENST00000369081.1_5'UTR|INPP5F_ENST00000369083.3_Frame_Shift_Ins_p.K76fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTGGTGGGCAAACTCCCAGG 0.3625 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ACADSB __UNKNOWN__ hg19 10 124794031 124794031 + DE_NOVO_START_OUT_FRAME SNP G G T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:124794031G>T ENST00000368869.4 + 2 ACADSB_ENST00000358776.4_Splice_Site_p.V68F|ACADSB_ENST00000496730.2_Splice_Site __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAAGAGTTCAGGTAAGTAAAT 0.40648379052369077 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false OR51E1 __UNKNOWN__ hg19 11 4664657 4664657 + DE_NOVO_START_OUT_FRAME SNP C C T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr11:4664657C>T ENST00000396952.5 + 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTGAATTCCACGCTTAGCAAG 0.486284289276808 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1416,7 +1416,7 @@ NARS2 __UNKNOWN__ hg19 11 78282425 78282425 + DE_NOVO_START_OUT_FRAME SNP G G C C11orf1 __UNKNOWN__ hg19 11 111753117 111753118 + Frame_Shift_Ins INS - - GT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr11:111753117_111753118insGT ENST00000530214.1 + 2 90 c.71_72insGT c.(70-72)acafs p.N25fs C11orf1_ENST00000528125.1_5'UTR|C11orf1_ENST00000260276.3_Frame_Shift_Ins_p.N25fs|C11orf1_ENST00000529270.1_Frame_Shift_Ins_p.N65fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTTTCCTCACAAACCCACAC 0.4425 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TMPRSS5 __UNKNOWN__ hg19 11 113565234 113565234 + DE_NOVO_START_OUT_FRAME SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr11:113565234G>A ENST00000536856.1 - 6 TMPRSS5_ENST00000299882.5_Missense_Mutation_p.R251C|TMPRSS5_ENST00000540540.1_DE_NOVO_START_OUT_FRAME|TMPRSS5_ENST00000545579.1_Missense_Mutation_p.R242C|TMPRSS5_ENST00000538955.1_Missense_Mutation_p.R207C|TMPRSS5_ENST00000544634.1_Intron|TMPRSS5_ENST00000544476.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCACCCAGCGTGGCGCTAGC 0.5586034912718204 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TMPRSS5 __UNKNOWN__ hg19 11 113565260 113565260 + DE_NOVO_START_IN_FRAME SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr11:113565260G>A ENST00000536856.1 - 6 TMPRSS5_ENST00000299882.5_Missense_Mutation_p.T242M|TMPRSS5_ENST00000545579.1_Missense_Mutation_p.T233M|TMPRSS5_ENST00000540540.1_DE_NOVO_START_IN_FRAME|TMPRSS5_ENST00000538955.1_Missense_Mutation_p.T198M|TMPRSS5_ENST00000544634.1_Intron|TMPRSS5_ENST00000544476.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCCCCACACGTGTGCCGGAA 0.5760598503740648 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -TAS2R43 __UNKNOWN__ hg19 12 11243924 11243935 + In_Frame_Del DEL TTCACC TTCACC - 867813065 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:11243924_11243929delTTCACC ENST00000531678.1 - 1 990 c.900_905delGGTGAA c.(898-906)tgggtgaaa>tga p.300_302WVK>* TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTTCTCTCCTTTCACCCAGTACCTCA 0.35714285714285715 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PRH1-TAS2R14:106707243|TAS2R43:259289|PRH1:5554|PRH1-PRR4:100533464 false true true false false false false false true false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000080005000402000210 1 false 147 rs867813065 11243924 false +TAS2R43 __UNKNOWN__ hg19 12 11243924 11243935 + In_Frame_Del DEL TTCACC TTCACC - 867813065 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:11243924_11243929delTTCACC ENST00000531678.1 - 1 990_995 c.900_905delGGTGAA c.(898-906)tgggtgaaa>tga p.300_302WVK>* TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTTCTCTCCTTTCACCCAGTACCTCA 0.35714285714285715 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PRH1-TAS2R14:106707243|TAS2R43:259289|PRH1:5554|PRH1-PRR4:100533464 false true true false false false false false true false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000080005000402000210 1 false 147 rs867813065 11243924 false OVCH1 __UNKNOWN__ hg19 12 29597130 29597131 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:29597130_29597131insA ENST00000318184.5 - 24 2965 c.2964_2965insT c.(2965-2967)aagfs p.K989fs OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTTCTGGCTTGGTCAGAAGA 0.3825 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false SCN8A __UNKNOWN__ hg19 12 52201139 52201140 + Frame_Shift_Ins INS - - C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:52201139_52201140insC ENST00000354534.6 + 27 6047 c.5869_5870insC c.(5869-5871)aaafs p.K1957fs SCN8A_ENST00000545061.1_Frame_Shift_Ins_p.K1916fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAAAGGAGAAACAGCAGCG 0.465 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false C12orf10 __UNKNOWN__ hg19 12 53699726 53699727 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:53699726_53699727insA ENST00000549488.1 + 2 205 c.35_36insA c.(34-36)gtgfs p.D13fs C12orf10_ENST00000267103.5_Frame_Shift_Ins_p.D176fs|C12orf10_ENST00000548632.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGGATGCTGTGGACAATGGG 0.515 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1584,7 +1584,7 @@ NADK2 __UNKNOWN__ hg19 5 36227619 36227619 + DE_NOVO_START_OUT_FRAME SNP T T C CCL28 __UNKNOWN__ hg19 5 43388500 43388500 + START_CODON_SNP SNP A A T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:43388500A>T ENST00000513525.1 - 2 309 c.2T>A c.(1-3)aTg>aAg p.M1K CCL28_ENST00000361115.4_Missense_Mutation_p.M48K|CCL28_ENST00000537013.1_Missense_Mutation_p.M48K __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GATGCGACACATATTCACTCT 0.4239401496259352 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false NNT __UNKNOWN__ hg19 5 43656769 43656770 + Frame_Shift_Ins INS - - T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:43656769_43656770insT ENST00000264663.5 + 16 2529 c.2308_2309insT c.(2308-2310)gccfs p.A770fs NNT_ENST00000344920.4_Frame_Shift_Ins_p.A770fs|NNT_ENST00000512996.2_Frame_Shift_Ins_p.A639fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCTGCCCCTCTCCT 0.415 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MRPS30 __UNKNOWN__ hg19 5 44809066 44809066 + START_CODON_SNP SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:44809066T>C ENST00000507110.1 + 1 40 c.2T>C c.(1-3)aTg>aCg p.M1T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGGCAAAGATGGCGGCGGCC 0.5910224438902744 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -GZMK __UNKNOWN__ hg19 5 54329753 54329756 + Nonstop_Mutation DEL AA AA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:54329753_54329754delAA ENST00000231009.2 + 5 863 c.794_795delAA c.(793-795)taafs p.*265fs CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CATACAAATTAAGTTACAAATA 0.39800995024875624 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +GZMK __UNKNOWN__ hg19 5 54329753 54329756 + Nonstop_Mutation DEL AA AA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:54329753_54329754delAA ENST00000231009.2 + 5 863_864 c.794_795delAA c.(793-795)taafs p.*265fs CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CATACAAATTAAGTTACAAATA 0.39800995024875624 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false AGGF1 __UNKNOWN__ hg19 5 76342200 76342201 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:76342200_76342201insA ENST00000312916.7 + 6 1281 c.899_900insA c.(898-900)ttcfs p.F300fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAAAAGCCTTCAGTGTTGAA 0.3725 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false FAM81B __UNKNOWN__ hg19 5 94785984 94785984 + Nonstop_Mutation SNP T T C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:94785984T>C ENST00000283357.5 + 10 1403 c.1357T>C c.(1357-1359)Taa>Caa p.*453Q __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCAGGAAGTATAAACCTTTTC 0.32418952618453867 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false SLCO4C1 __UNKNOWN__ hg19 5 101572564 101572564 + Nonstop_Mutation SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:101572564A>G ENST00000310954.6 - 13 2460 c.2173T>C c.(2173-2175)Tga>Cga p.*725R __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCCCATTTCACCCTTCTTTT 0.3192019950124688 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1634,7 +1634,7 @@ RHAG __UNKNOWN__ hg19 6 49604523 49604523 + START_CODON_SNP SNP C C A __UNKNO EFHC1 __UNKNOWN__ hg19 6 52285209 52285209 + START_CODON_SNP SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:52285209A>G ENST00000371068.5 + 1 104 c.1A>G c.(1-3)Atg>Gtg p.M1V EFHC1_ENST00000433625.2_5'UTR|EFHC1_ENST00000491749.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCGGCTGCAATGGTGTCCAA 0.6134663341645885 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false IMPG1 __UNKNOWN__ hg19 6 76782204 76782204 + START_CODON_SNP SNP A A T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:76782204A>T ENST00000369950.3 - 1 192 c.2T>A c.(1-3)aTg>aAg p.M1K IMPG1_ENST00000369963.3_START_CODON_SNP_p.M1K __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCCAAATACATTCTGGCTTT 0.3167082294264339 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false RIPPLY2 __UNKNOWN__ hg19 6 84567107 84567107 + Nonstop_Mutation SNP A A C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:84567107A>C ENST00000369689.1 + 4 537 c.386A>C c.(385-387)tAa>tCa p.*129S RIPPLY2_ENST00000369687.1_Nonstop_Mutation_p.*71S __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGTGAAAATTAATCTGATTAG 0.2793017456359102 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -RARS2 __UNKNOWN__ hg19 6 88255395 88255400 + In_Frame_Del DEL TTT TTT - 757743894 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:88255395_88255397delTTT ENST00000369536.5 - 7 521 c.472_474delAAA c.(472-474)aaadel p.K158del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTAAAGCTTCTTTGAGATTTGCT 0.2903225806451613 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false RARS2:57038 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false 0.999966,3.4343e-005 false false false DIV 0x050000000005040402000200 1 false 144 rs757743894 88255395 true +RARS2 __UNKNOWN__ hg19 6 88255395 88255400 + In_Frame_Del DEL TTT TTT - 757743894 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:88255395_88255397delTTT ENST00000369536.5 - 7 521_523 c.472_474delAAA c.(472-474)aaadel p.K158del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTAAAGCTTCTTTGAGATTTGCT 0.2903225806451613 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false RARS2:57038 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false 0.999966,3.4343e-005 false false false DIV 0x050000000005040402000200 1 false 144 rs757743894 88255395 true AK9 __UNKNOWN__ hg19 6 109954114 109954114 + Nonstop_Mutation SNP T T A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:109954114T>A ENST00000285397.5 - 12 1348 c.1266A>T c.(1264-1266)taA>taT p.*422Y AK9_ENST00000368948.2_Intron|AK9_ENST00000424296.2_Intron|AK9_ENST00000341338.6_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGACAGATAGTTAGTTAGTCA 0.33915211970074816 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false RFX6 __UNKNOWN__ hg19 6 117249986 117249987 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:117249986_117249987insA ENST00000332958.2 + 18 2479 c.2463_2464insA c.(2464-2466)gttfs p.V822fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAATCAGCACGTTTCTGTCA 0.3925 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false TAAR8 __UNKNOWN__ hg19 6 132874859 132874859 + Splice_Site SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:132874859A>G ENST00000275200.1 + 1 1028 c.1028A>G c.(1027-1029)tAa>tGa p.*343* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTTTTAGAATAAGTTTAAGCA 0.26184538653366585 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ SILENT false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -1648,7 +1648,7 @@ SDIM1 __UNKNOWN__ hg19 6 166308924 166308924 + DE_NOVO_START_OUT_FRAME SNP G G ABCB5 __UNKNOWN__ hg19 7 20685486 20685487 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:20685486_20685487insA ENST00000404938.2 + 8 1438 c.786_787insA c.(787-789)gagfs p.E263fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TAGGGCCCAGGAGAAAGAAC 0.3725 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MALSU1 __UNKNOWN__ hg19 7 23338972 23338972 + START_CODON_SNP SNP A A G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:23338972A>G ENST00000466681.1 + 1 154 c.1A>G c.(1-3)Atg>Gtg p.M1V MALSU1_ENST00000479974.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGCTGCTGCTATGGGGCCGGG 0.6708229426433915 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false STK31 __UNKNOWN__ hg19 7 23749905 23749905 + START_CODON_SNP SNP A A T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:23749905A>T ENST00000355870.3 + 1 120 c.1A>T c.(1-3)Atg>Ttg p.M1L STK31_ENST00000433467.2_START_CODON_SNP_p.M1L __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAAGTCCAGTATGTGGGTCCA 0.6234413965087282 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -HOXA5 __UNKNOWN__ hg19 7 27181456 27181459 + Nonstop_Mutation DEL AG AG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:27181456_27181457delAG ENST00000222726.3 - 2 873 c.810_811delCT c.(808-810)cccfs p.*271fs RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA5_ENST00000520854.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCAGATACTCAGGGACGGAAGG 0.4651741293532338 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +HOXA5 __UNKNOWN__ hg19 7 27181456 27181459 + Nonstop_Mutation DEL AG AG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:27181456_27181457delAG ENST00000222726.3 - 2 873_874 c.810_811delCT c.(808-810)cccfs p.*271fs RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA5_ENST00000520854.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCAGATACTCAGGGACGGAAGG 0.4651741293532338 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false RP9 __UNKNOWN__ hg19 7 33134848 33134849 + Nonstop_Mutation DEL A A - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:33134848delA ENST00000297157.3 - 6 683 c.664delT c.(664-666)tgafs p.*222fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CATCCTTGTCACTCTGAGTCA 0.4488778054862843 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false ABCA13 __UNKNOWN__ hg19 7 48278997 48278998 + Frame_Shift_Ins INS - - GGTA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:48278997_48278998insGGTA ENST00000435803.1 + 9 1081 c.1057_1058insGGTA c.(1057-1059)caafs p.Q353fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGAGTCTACCAACAGGTGCT 0.495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false VSTM2A __UNKNOWN__ hg19 7 54610426 54610426 + START_CODON_SNP SNP G G A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr7:54610426G>A ENST00000404951.1 + 1 318 c.3G>A c.(1-3)atG>atA p.M1I VSTM2A_ENST00000407838.3_START_CODON_SNP_p.M1I|VSTM2A_ENST00000302287.3_START_CODON_SNP_p.M1I|VSTM2A_ENST00000402613.3_START_CODON_SNP_p.M1I|VSTM2A_ENST00000402026.2_5'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTTTTGGAATGATGGGGATCT 0.4837905236907731 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf index 64252fa5fb8..2f511c43085 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf @@ -25,7 +25,7 @@ ##FORMAT= ##Funcotator Version=0.0.4 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic v84 | CosmicFusion v84 | CosmicTissue v83 | DNARepairGenes 20180524T145835 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Oreganno 20160119 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 ##Funcotator Version=0.0.5 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 -##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##Hyb(High)=Hyb(High)|Hybridization|3310|11184 ##Hyb(Low)=Hyb(Low)|Hybridization|3436|1823 @@ -809,7 +809,7 @@ chr1 7999982 variant.617 G A . PASS FUNCOTATION=[TNFRSF9|hg19|chr1|7999982|79999 chr1 8021973 exm-rs35675666 G T . PASS FUNCOTATION=[PARK7|hg19|chr1|8021973|8021973|FIVE_PRIME_UTR||SNP|G|G|T|g.chr1:8021973G>T|ENST00000377491.1|+|1|||||0.6583541147132169|GCGGGGCCTGGGTCGGGGCCG|PARK7_ENST00000493678.1_INTRON/PARK7_ENST00000338639.5_INTRON/PARK7_ENST00000377493.5_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8518_%2C_._%2C_0.1482|false|false|1||false|true|true|PARK7:11315|true|true|true|true|true|false|true|false|false|false|false|false|false|false|false|true|true|false|true|false|35675666|8021973|false|false|0|true|0|false|0.816402_%2C_._%2C_0.183598|false|false|false|SNV|true|0x0501280a0005170537020100|1|false|126|rs35675666] chr1 8029464 variant.620 G A . PASS FUNCOTATION=[PARK7|hg19|chr1|8029464|8029464|SPLICE_SITE|SILENT|SNP|G|G|A|g.chr1:8029464G>A|ENST00000493678.1|+|4|319|c.252G>A|c.(250-252)gaG>gaA|p.E84E|0.3192019950124688|ATTTATCTGAGGTAAAAAATT|PARK7_ENST00000377491.1_SPLICE_SITE_p.E84E/PARK7_ENST00000338639.5_SPLICE_SITE_p.E84E/PARK7_ENST00000377488.1_SPLICE_SITE_p.E84E/PARK7_ENST00000377493.5_INTRON/PARK7_ENST00000497113.1_SPLICE_SITE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|true|749774196|8029464|false|false|0|false|0|true||false|false|false|SNV|false|0x050000080305000402000100|1|false|144|rs749774196] chr1 8029464 variant.620 G A . PASS FUNCOTATION=[PARK7|hg19|chr1|8029464|8029464|SPLICE_SITE|SILENT|SNP|G|G|A|g.chr1:8029464G>A|ENST00000493678.1|+|4|319|c.252G>A|c.(250-252)gaG>gaA|p.E84E|0.3192019950124688|ATTTATCTGAGGTAAAAAATT|PARK7_ENST00000377491.1_SPLICE_SITE_p.E84E/PARK7_ENST00000338639.5_SPLICE_SITE_p.E84E/PARK7_ENST00000377488.1_SPLICE_SITE_p.E84E/PARK7_ENST00000377493.5_INTRON/PARK7_ENST00000497113.1_SPLICE_SITE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|true|749774196|8029464|false|false|0|false|0|true||false|false|false|SNV|false|0x050000080305000402000100|1|false|144|rs749774196] -chr1 8045014 indel.625 GGCC G . PASS FUNCOTATION=[PARK7|hg19|chr1|8045015|8045017|IN_FRAME_DEL||DEL|GCC|GCC|-|g.chr1:8045015_8045017delGCC|ENST00000493678.1|+|7|537|c.471_473delGCC|c.(469-474)gggcct>ggt|p.P158del|0.4466501240694789|CAAGCCGGGGGCCTGGGACCAGC|PARK7_ENST00000377491.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000338639.5_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377488.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377493.5_IN_FRAME_DEL_p.P138del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|764877312|8045015|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs764877312] +chr1 8045014 indel.625 GGCC G . PASS FUNCOTATION=[PARK7|hg19|chr1|8045015|8045017|IN_FRAME_DEL||DEL|GCC|GCC|-|g.chr1:8045015_8045017delGCC|ENST00000493678.1|+|7|537_539|c.471_473delGCC|c.(469-474)gggcct>ggt|p.P158del|0.4466501240694789|CAAGCCGGGGGCCTGGGACCAGC|PARK7_ENST00000377491.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000338639.5_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377488.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377493.5_IN_FRAME_DEL_p.P138del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|764877312|8045015|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs764877312] chr1 8073830 exm11005 C T . PASS FUNCOTATION=[ERRFI1|hg19|chr1|8073830|8073830|THREE_PRIME_UTR||SNP|C|C|T|g.chr1:8073830C>T|ENST00000469499.1|-|3|||||0.48877805486284287|TTGTCTTCATCGGAGTTAGGA|ERRFI1_ENST00000474874.1_INTRON/ERRFI1_ENST00000377482.5_MISSENSE_p.D277N/ERRFI1_ENST00000467067.1_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 8073919 exm11011 C T . PASS FUNCOTATION=[ERRFI1|hg19|chr1|8073919|8073919|THREE_PRIME_UTR||SNP|C|C|T|g.chr1:8073919C>T|ENST00000469499.1|-|3|||||0.46384039900249374|ATGAGACCTTCTTAATCTTCG|ERRFI1_ENST00000474874.1_INTRON/ERRFI1_ENST00000377482.5_MISSENSE_p.R247K/ERRFI1_ENST00000467067.1_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 8073925 exm11013 C T . PASS FUNCOTATION=[ERRFI1|hg19|chr1|8073925|8073925|THREE_PRIME_UTR||SNP|C|C|T|g.chr1:8073925C>T|ENST00000469499.1|-|3|||||0.46384039900249374|CCTTCTTAATCTTCGGTGGGT|ERRFI1_ENST00000474874.1_INTRON/ERRFI1_ENST00000377482.5_MISSENSE_p.R245K/ERRFI1_ENST00000467067.1_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -914,7 +914,7 @@ chr1 11901592 rs198415 T C . PASS FUNCOTATION=[CLCN6|hg19|chr1|11901592|11901592 chr1 11906068 exm15531 A G . PASS FUNCOTATION=[NPPA|hg19|chr1|11906068|11906068|NONSTOP||SNP|A|A|G|g.chr1:11906068A>G|ENST00000376480.3|-|3|553|c.454T>C|c.(454-456)Tga>Cga|p.*152R|0.4937655860349127|TGTTATCTTCAGTACTGCAAA|NPPA_ENST00000376476.1_NONSTOP_p.*102R/NPPA-AS1_ENST00000446542.1_RNA/NPPA-AS1_ENST00000400892.2_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8209_%2C_0.1791|false|false|1||false|true|false|NPPA:4878_%7C_NPPA-AS1:100379251|true|true|true|true|true|false|false|false|false|false|false|false|false|false|false|true|true|false|false|true|5065|11906068|false|false|0|true|0|false|0.737688_%2C_0.262312|true|false|false|SNV|true|0x05013808020515053f000100|1|false|52|rs5065] chr1 11906068 rs5065 A G . PASS FUNCOTATION=[NPPA|hg19|chr1|11906068|11906068|NONSTOP||SNP|A|A|G|g.chr1:11906068A>G|ENST00000376480.3|-|3|553|c.454T>C|c.(454-456)Tga>Cga|p.*152R|0.4937655860349127|TGTTATCTTCAGTACTGCAAA|NPPA_ENST00000376476.1_NONSTOP_p.*102R/NPPA-AS1_ENST00000446542.1_RNA/NPPA-AS1_ENST00000400892.2_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8209_%2C_0.1791|false|false|1||false|true|false|NPPA:4878_%7C_NPPA-AS1:100379251|true|true|true|true|true|false|false|false|false|false|false|false|false|false|false|true|true|false|false|true|5065|11906068|false|false|0|true|0|false|0.737688_%2C_0.262312|true|false|false|SNV|true|0x05013808020515053f000100|1|false|52|rs5065] chr1 12025599 exm15795 C G . PASS FUNCOTATION=[PLOD1|hg19|chr1|12025599|12025599|NONSENSE||SNP|C|C|G|g.chr1:12025599C>G|ENST00000196061.4|+|14|1560|c.1533C>G|c.(1531-1533)taC>taG|p.Y511*|0.6384039900249376|TAGACAGCTACCGCACCACCC|PLOD1_ENST00000376369.3_NONSENSE_p.Y558*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 12069756 indel.888 CACTT C . PASS FUNCOTATION=[MFN2|hg19|chr1|12069757|12069760|FRAME_SHIFT_DEL||DEL|ACTT|ACTT|-|g.chr1:12069757_12069760delACTT|ENST00000235329.5|+|18|2499|c.2178_2181delACTT|c.(2176-2181)tcacttfs|p.L727fs|0.5693069306930693|TTCTTGACTCACTTCAGAGCAAAG|MFN2_ENST00000444836.1_FRAME_SHIFT_DEL_p.L727fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MFN2:9927|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|772270096|12069757|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs772270096] +chr1 12069756 indel.888 CACTT C . PASS FUNCOTATION=[MFN2|hg19|chr1|12069757|12069760|FRAME_SHIFT_DEL||DEL|ACTT|ACTT|-|g.chr1:12069757_12069760delACTT|ENST00000235329.5|+|18|2499_2502|c.2178_2181delACTT|c.(2176-2181)tcacttfs|p.L727fs|0.5693069306930693|TTCTTGACTCACTTCAGAGCAAAG|MFN2_ENST00000444836.1_FRAME_SHIFT_DEL_p.L727fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MFN2:9927|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|772270096|12069757|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs772270096] chr1 12082195 exm15947 C A . PASS FUNCOTATION=[MIIP|hg19|chr1|12082195|12082195|NONSENSE||SNP|C|C|A|g.chr1:12082195C>A|ENST00000235332.4|+|3|327|c.158C>A|c.(157-159)tCg>tAg|p.S53*|0.6483790523690773|GAGACTCCATCGACCCCAGAG|MIIP_ENST00000436478.2_NONSENSE_p.S53*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 12090140 exm16010 C T . PASS FUNCOTATION=[MIIP|hg19|chr1|12090140|12090140|NONSENSE||SNP|C|C|T|g.chr1:12090140C>T|ENST00000235332.4|+|8|1070|c.901C>T|c.(901-903)Cga>Tga|p.R301*|0.6533665835411472|CATCCACCGGCGAAAGAGCTT|MIIP_ENST00000436478.2_INTRON/MIIP_ENST00000466860.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 12318010 variant.909 T G . PASS FUNCOTATION=[VPS13D|hg19|chr1|12318010|12318010|NONSENSE||SNP|T|T|G|g.chr1:12318010T>G|ENST00000358136.3|+|10|1090|c.960T>G|c.(958-960)taT>taG|p.Y320*|0.4164588528678304|AATGGTGGTATTTTGCTTTGA|VPS13D_ENST00000356315.4_NONSENSE_p.Y320*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1078,7 +1078,7 @@ chr1 20976994 indel.1467 TG T . PASS FUNCOTATION=[PINK1|hg19|chr1|20976995|20976 chr1 20978058 exm2264808 G A . PASS FUNCOTATION=[PINK1-AS|hg19|chr1|20978058|20978058|RNA||SNP|G|G|A|g.chr1:20978058G>A|ENST00000451424.1|-|||c.e1-628C>T|||0.4239401496259352|CCATTTCAGTGATTCCCACCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 20978058 rs650616 G A . PASS FUNCOTATION=[PINK1-AS|hg19|chr1|20978058|20978058|RNA||SNP|G|G|A|g.chr1:20978058G>A|ENST00000451424.1|-|||c.e1-628C>T|||0.4239401496259352|CCATTTCAGTGATTCCCACCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 20987879 exm27256 A C . PASS FUNCOTATION=[DDOST|hg19|chr1|20987879|20987879|FIVE_PRIME_UTR||SNP|A|A|C|g.chr1:20987879A>C|ENST00000602624.2|-|1|||||0.6508728179551122|GCACGTGCACACCGGAAGTAC|DDOST_ENST00000375048.3_MISSENSE_p.C6G/DDOST_ENST00000415136.2_MISSENSE_p.C6G|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 20998552 indel.1474 CAG C . PASS FUNCOTATION=[KIF17|hg19|chr1|20998553|20998554|FRAME_SHIFT_DEL||DEL|AG|AG|-|g.chr1:20998553_20998554delAG|ENST00000247986.2|-|12|2912|c.2599_2600delCT|c.(2599-2601)ctgfs|p.L867fs|0.5696517412935324|CCTGCGAATCAGGGGCTGCACC|KIF17_ENST00000400463.3_FRAME_SHIFT_DEL_p.L867fs/KIF17_ENST00000375044.1_FRAME_SHIFT_DEL_p.L767fs/KIF17_ENST00000490034.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 20998552 indel.1474 CAG C . PASS FUNCOTATION=[KIF17|hg19|chr1|20998553|20998554|FRAME_SHIFT_DEL||DEL|AG|AG|-|g.chr1:20998553_20998554delAG|ENST00000247986.2|-|12|2912_2913|c.2599_2600delCT|c.(2599-2601)ctgfs|p.L867fs|0.5696517412935324|CCTGCGAATCAGGGGCTGCACC|KIF17_ENST00000400463.3_FRAME_SHIFT_DEL_p.L867fs/KIF17_ENST00000375044.1_FRAME_SHIFT_DEL_p.L767fs/KIF17_ENST00000490034.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 21047725 rs659046 A G . PASS FUNCOTATION=[SH2D5|hg19|chr1|21047725|21047725|THREE_PRIME_UTR||SNP|A|A|G|g.chr1:21047725A>G|ENST00000375031.1|-|9|||||0.5810473815461347|TCAGATACATATGAGAAACAG|SH2D5_ENST00000460804.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 21544601 rs3026913 C T . PASS FUNCOTATION=[ECE1|hg19|chr1|21544601|21544601|THREE_PRIME_UTR||SNP|C|C|T|g.chr1:21544601C>T|ENST00000415912.2|-|19|||||0.6184538653366584|GAGTCTGCTACTGGAGAAGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 21742614 rs10916982 T C . PASS FUNCOTATION=[RP11-293F5.1|hg19|chr1|21742614|21742614|LINCRNA||SNP|T|T|C|g.chr1:21742614T>C|ENST00000444647.1|+|||c.e1+186T>C|||0.5311720698254364|CCCTGAGAGATCCCAACAGTC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1120,7 +1120,7 @@ chr1 25908805 psy_rs6598889 T C . PASS FUNCOTATION=[RP11-70P17.1|hg19|chr1|25908 chr1 25914219 rs7546822 T C . PASS FUNCOTATION=[RP11-70P17.1|hg19|chr1|25914219|25914219|LINCRNA||SNP|T|T|C|g.chr1:25914219T>C|ENST00000412797.1|+|||c.e2-2441T>C|||0.48877805486284287|AAAGAGTTACTGAGAACTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 26161571 indel.1796 CT C . PASS FUNCOTATION=[AUNIP|hg19|chr1|26161572|26161572|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:26161572delT|ENST00000374298.3|-|3|1042|c.986delA|c.(985-987)cagfs|p.Q329fs|0.44139650872817954|CCCATCCTCCTGGCACTGAGC|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.Q329fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 26161629 var_1_26161629 GT G . PASS FUNCOTATION=[AUNIP|hg19|chr1|26161630|26161630|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:26161630delT|ENST00000374298.3|-|3|984|c.928delA|c.(928-930)accfs|p.T310fs|0.4339152119700748|CAGTTATTGGTTACATCTTGA|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.T310fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 26161798 indel.1800 AGG A . PASS FUNCOTATION=[AUNIP|hg19|chr1|26161799|26161800|FRAME_SHIFT_DEL||DEL|GG|GG|-|g.chr1:26161799_26161800delGG|ENST00000374298.3|-|3|815|c.758_759delCC|c.(757-762)tcctggfs|p.S253fs|0.4527363184079602|CTCCATTCCAGGATTCCCTGTA|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.S253fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 26161798 indel.1800 AGG A . PASS FUNCOTATION=[AUNIP|hg19|chr1|26161799|26161800|FRAME_SHIFT_DEL||DEL|GG|GG|-|g.chr1:26161799_26161800delGG|ENST00000374298.3|-|3|815_816|c.758_759delCC|c.(757-762)tcctggfs|p.S253fs|0.4527363184079602|CTCCATTCCAGGATTCCCTGTA|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.S253fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 26161915 indel.1804 TG T . PASS FUNCOTATION=[AUNIP|hg19|chr1|26161916|26161916|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr1:26161916delG|ENST00000374298.3|-|3|698|c.642delC|c.(640-642)cacfs|p.H214fs|0.4488778054862843|GTAGTTTGGTGTGTTTCTCCA|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.H214fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 26164008 indel.1810 AG A . PASS FUNCOTATION=[AUNIP|hg19|chr1|26164009|26164009|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr1:26164009delG|ENST00000374298.3|-|2|171|c.115delC|c.(115-117)ctcfs|p.L39fs|0.39650872817955113|CCAGGAAGGAGTGTTAGCATT|AUNIP_ENST00000538789.1_FRAME_SHIFT_DEL_p.L39fs/AUNIP_ENST00000481602.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 26301006 indel.1816 AC A . PASS FUNCOTATION=[PAFAH2|hg19|chr1|26301007|26301007|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:26301007delC|ENST00000374282.3|-|9|1074|c.893delG|c.(892-894)tgtfs|p.C298fs|0.4538653366583541|ATGCTGGGCACATATCTTCTT|PAFAH2_ENST00000374284.1_FRAME_SHIFT_DEL_p.C298fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1183,21 +1183,21 @@ chr1 43004894 indel.2772 CA C . PASS FUNCOTATION=[CCDC30|hg19|chr1|43004895|4300 chr1 43021827 indel.2775 TC T . PASS FUNCOTATION=[CCDC30|hg19|chr1|43021828|43021828|SPLICE_SITE|FRAME_SHIFT_DEL|DEL|C|C|-|g.chr1:43021828delC|ENST00000340612.4|+|4|426|c.427delC|c.(427-429)cccfs|p.K144fs|0.38902743142144636|TGCACCAAGTCCCAAATTAGG|CCDC30_ENST00000507855.1_INTRON/CCDC30_ENST00000428554.2_SPLICE_SITE_p.K144fs/CCDC30_ENST00000342022.4_SPLICE_SITE_p.K144fs/CCDC30_ENST00000390640.4_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 43232984 exm51112 T C . PASS FUNCOTATION=[C1orf50|hg19|chr1|43232984|43232984|START_CODON_SNP||SNP|T|T|C|g.chr1:43232984T>C|ENST00000372525.5|+|1|45|c.2T>C|c.(1-3)aTg>aCg|p.M1T|0.6957605985037406|GGCGCTGTCATGGAGGACGCC|C1orf50_ENST00000536543.1_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.9996_%2C_._%2C_0.0003994|false|false|0||false|false|false|P3H1:64175_%7C_C1orf50:79078|false|true|false|true|true|false|false|false|false|false|false|true|false|false|false|false|false|false|true|true|200116115|43232984|false|false|0|false|0|false|0.999622_%2C_0.000171715_%2C_0.000206058|false|false|false|SNV|true|0x050000020a05040436000100|1|false|137|rs200116115] chr1 43610910 rs626842 T G . PASS FUNCOTATION=[FAM183A|hg19|chr1|43610910|43610910|FIVE_PRIME_UTR||SNP|T|T|G|g.chr1:43610910T>G|ENST00000410048.1|+|1|||||0.47880299251870323|TGCAGGGCCATTGACAGAGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 43783609 indel.2866 CGGAA C . PASS FUNCOTATION=[TIE1|hg19|chr1|43783610|43783613|FRAME_SHIFT_DEL||DEL|GGAA|GGAA|-|g.chr1:43783610_43783613delGGAA|ENST00000372476.3|+|17|2867|c.2789_2792delGGAA|c.(2788-2793)cggaaafs|p.R930fs|0.5668316831683168|GATTTTCTGCGGAAAAGCCGGGTC|TIE1_ENST00000433781.2_FRAME_SHIFT_DEL_p.R575fs/TIE1_ENST00000473014.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 43783609 indel.2866 CGGAA C . PASS FUNCOTATION=[TIE1|hg19|chr1|43783610|43783613|FRAME_SHIFT_DEL||DEL|GGAA|GGAA|-|g.chr1:43783610_43783613delGGAA|ENST00000372476.3|+|17|2867_2870|c.2789_2792delGGAA|c.(2788-2793)cggaaafs|p.R930fs|0.5668316831683168|GATTTTCTGCGGAAAAGCCGGGTC|TIE1_ENST00000433781.2_FRAME_SHIFT_DEL_p.R575fs/TIE1_ENST00000473014.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 43854091 exm52079 C G . PASS FUNCOTATION=[MED8|hg19|chr1|43854091|43854091|FIVE_PRIME_UTR||SNP|C|C|G|g.chr1:43854091C>G|ENST00000372455.4|-|2|||||0.4837905236907731|CAAGCTGCTTCTCCTCTCTCT|MED8_ENST00000372457.4_MISSENSE_p.E5D/MED8_ENST00000290663.6_MISSENSE_p.E5D/RP1-92O14.6_ENST00000436713.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 44445667 rs3762423 T C . PASS FUNCOTATION=[B4GALT2|hg19|chr1|44445667|44445667|FIVE_PRIME_UTR||SNP|T|T|C|g.chr1:44445667T>C|ENST00000356836.6|+|1|||||0.6384039900249376|GTGTGAGCTGTCTGAGAGTCT|B4GALT2_ENST00000372324.1_INTRON/B4GALT2_ENST00000434555.2_INTRON/B4GALT2_ENST00000309519.7_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 45205606 exm53931 T A . PASS FUNCOTATION=[KIF2C|hg19|chr1|45205606|45205606|START_CODON_SNP||SNP|T|T|A|g.chr1:45205606T>A|ENST00000372224.4|+|1|115|c.2T>A|c.(1-3)aTg>aAg|p.M1K|0.5835411471321695|ACTCTCCGAATGGCCATGGAC|KIF2C_ENST00000372218.4_START_CODON_SNP_p.M1K/KIF2C_ENST00000493027.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 45241113 rs11211031 T C . PASS FUNCOTATION=[RPS8|hg19|chr1|45241113|45241113|FIVE_PRIME_UTR||SNP|T|T|C|g.chr1:45241113T>C|ENST00000396651.3|+|1|||||0.5985037406483791|GAGACCCTCCTAGGCTCGTGG|RP11-269F19.2_ENST00000428791.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 45477940 variant.3034 G A . PASS FUNCOTATION=[UROD|hg19|chr1|45477940|45477940|START_CODON_SNP||SNP|G|G|A|g.chr1:45477940G>A|ENST00000246337.4|+|1|122|c.3G>A|c.(1-3)atG>atA|p.M1I|0.543640897755611|AGCTGACCATGGAAGCGAATG|UROD_ENST00000494399.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 45965246 indel.3113 ATCCAGCTG A . PASS FUNCOTATION=[CCDC163P|hg19|chr1|45965247|45965254|FRAME_SHIFT_DEL||DEL|TCCAGCTG|TCCAGCTG|-|g.chr1:45965247_45965254delTCCAGCTG|ENST00000432082.1|-|1|401|c.28_35delCAGCTGGA|c.(28-36)cagctggatfs|p.Q10fs|0.5465686274509803|GAGAAGCACATCCAGCTGCTCAAACCAG|CCDC163P_ENST00000488405.2_FRAME_SHIFT_DEL_p.Q10fs/CCDC163P_ENST00000490551.3_FRAME_SHIFT_DEL_p.Q10fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 45965246 indel.3113 ATCCAGCTG A . PASS FUNCOTATION=[CCDC163P|hg19|chr1|45965247|45965254|FRAME_SHIFT_DEL||DEL|TCCAGCTG|TCCAGCTG|-|g.chr1:45965247_45965254delTCCAGCTG|ENST00000432082.1|-|1|401_408|c.28_35delCAGCTGGA|c.(28-36)cagctggatfs|p.Q10fs|0.5465686274509803|GAGAAGCACATCCAGCTGCTCAAACCAG|CCDC163P_ENST00000488405.2_FRAME_SHIFT_DEL_p.Q10fs/CCDC163P_ENST00000490551.3_FRAME_SHIFT_DEL_p.Q10fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 45974886 exm55303 G C . PASS FUNCOTATION=[MMACHC|hg19|chr1|45974886|45974886|NONSTOP||SNP|G|G|C|g.chr1:45974886G>C|ENST00000401061.4|+|4|1128|c.848G>C|c.(847-849)tGa>tCa|p.*283S|0.5112219451371571|CCTGGCCCTTGATTTTCTCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MMACHC:25974|false|true|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|true|201025783|45974886|false|false|0|false|0|false|0.999244_%2C_0.000240401_%2C_0.000515145|false|false|false|SNV|true|0x050000000205040416000100|1|false|137|rs201025783] chr1 46032295 var_1_46032295 GC G . PASS FUNCOTATION=[AKR1A1|hg19|chr1|46032296|46032296|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:46032296delC|ENST00000372070.3|+|4|886|c.140delC|c.(139-141)gctfs|p.A47fs|0.5261845386533666|ATTGATTGTGCTGCTATCTAC|AKR1A1_ENST00000351829.4_FRAME_SHIFT_DEL_p.A47fs/AKR1A1_ENST00000471651.1_FRAME_SHIFT_DEL_p.A47fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 46086465 indel.3153 CTT C . PASS FUNCOTATION=[CCDC17|hg19|chr1|46086466|46086467|FRAME_SHIFT_DEL||DEL|TT|TT|-|g.chr1:46086466_46086467delTT|ENST00000528266.1|-|12|1788|c.1638_1639delAA|c.(1636-1638)gcafs|p.D548fs|0.5597014925373134|GCTGCATCTCTTGCATTCACCA|CCDC17_ENST00000421127.2_FRAME_SHIFT_DEL_p.D539fs/CCDC17_ENST00000445048.2_INTRON/CCDC17_ENST00000343901.2_FRAME_SHIFT_DEL_p.D516fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 46086465 indel.3153 CTT C . PASS FUNCOTATION=[CCDC17|hg19|chr1|46086466|46086467|FRAME_SHIFT_DEL||DEL|TT|TT|-|g.chr1:46086466_46086467delTT|ENST00000528266.1|-|12|1788_1789|c.1638_1639delAA|c.(1636-1638)gcafs|p.D548fs|0.5597014925373134|GCTGCATCTCTTGCATTCACCA|CCDC17_ENST00000421127.2_FRAME_SHIFT_DEL_p.D539fs/CCDC17_ENST00000445048.2_INTRON/CCDC17_ENST00000343901.2_FRAME_SHIFT_DEL_p.D516fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46087133 indel.3158 TC T . PASS FUNCOTATION=[CCDC17|hg19|chr1|46087134|46087134|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:46087134delC|ENST00000528266.1|-|10|1356|c.1207delG|c.(1207-1209)gatfs|p.D403fs|0.600997506234414|CGCAGGAAATCATAGAAAATG|CCDC17_ENST00000421127.2_FRAME_SHIFT_DEL_p.D394fs/CCDC17_ENST00000445048.2_INTRON/CCDC17_ENST00000343901.2_FRAME_SHIFT_DEL_p.D371fs/CCDC17_ENST00000464739.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46120883 indel.3165 CA C . PASS FUNCOTATION=[GPBP1L1|hg19|chr1|46120884|46120884|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:46120884delA|ENST00000290795.3|-|4|1391|c.168delT|c.(166-168)aatfs|p.N56fs|0.4014962593516209|GTAGGGGACCATTGTTAAAAA|GPBP1L1_ENST00000355105.3_FRAME_SHIFT_DEL_p.N56fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46125880 rs3811436 T C . PASS FUNCOTATION=[GPBP1L1|hg19|chr1|46125880|46125880|FIVE_PRIME_UTR||SNP|T|T|C|g.chr1:46125880T>C|ENST00000290795.3|-|2|||||0.428927680798005|TCTGTGGTCCTGTTTCTGAAC|GPBP1L1_ENST00000355105.3_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46153203 rs3013595 G A . PASS FUNCOTATION=[TMEM69|hg19|chr1|46153203|46153203|FIVE_PRIME_UTR||SNP|G|G|A|g.chr1:46153203G>A|ENST00000372025.4|+|1|||||0.5012468827930174|ACACGGAAGGGCACTAAAATT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 46158964 indel.3168 CAT C . PASS FUNCOTATION=[TMEM69|hg19|chr1|46158965|46158966|FRAME_SHIFT_DEL||DEL|AT|AT|-|g.chr1:46158965_46158966delAT|ENST00000372025.4|+|3|1288|c.132_133delAT|c.(130-135)ccatgtfs|p.C45fs|0.4129353233830846|ACTTTTCCCCATGTCCAAGGCC|TMEM69_ENST00000496366.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 46158964 indel.3168 CAT C . PASS FUNCOTATION=[TMEM69|hg19|chr1|46158965|46158966|FRAME_SHIFT_DEL||DEL|AT|AT|-|g.chr1:46158965_46158966delAT|ENST00000372025.4|+|3|1288_1289|c.132_133delAT|c.(130-135)ccatgtfs|p.C45fs|0.4129353233830846|ACTTTTCCCCATGTCCAAGGCC|TMEM69_ENST00000496366.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46159031 indel.3170 AT A . PASS FUNCOTATION=[TMEM69|hg19|chr1|46159032|46159032|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:46159032delT|ENST00000372025.4|+|3|1355|c.199delT|c.(199-201)tccfs|p.S67fs|0.42144638403990026|CTATCATACATCCCCCTGCAG|TMEM69_ENST00000496366.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46543210 indel.3212 CT C . PASS FUNCOTATION=[PIK3R3|hg19|chr1|46543211|46543211|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:46543211delT|ENST00000262741.5|-|3|981|c.290delA|c.(289-291)cagfs|p.Q97fs|0.3516209476309227|ATAATCTCCCTGCATTTTTGT|PIK3R3_ENST00000420542.1_FRAME_SHIFT_DEL_p.Q97fs/PIK3R3_ENST00000372006.1_FRAME_SHIFT_DEL_p.Q97fs/PIK3R3_ENST00000423209.1_FRAME_SHIFT_DEL_p.Q97fs/PIK3R3_ENST00000354242.4_FRAME_SHIFT_DEL_p.Q97fs/PIK3R3_ENST00000340332.6_FRAME_SHIFT_DEL_p.Q61fs/PIK3R3_ENST00000540385.1_FRAME_SHIFT_DEL_p.Q143fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 46598273 rs1707303 A C . PASS FUNCOTATION=[PIK3R3|hg19|chr1|46598273|46598273|FIVE_PRIME_UTR||SNP|A|A|C|g.chr1:46598273A>C|ENST00000262741.5|-|1|||||0.6708229426433915|AACCAACCCGACCGCACCAAC|PIK3R3_ENST00000420542.1_INTRON/PIK3R3_ENST00000372006.1_INTRON/PIK3R3_ENST00000423209.1_FIVE_PRIME_UTR/PIK3R3_ENST00000354242.4_INTRON/PIK3R3_ENST00000340332.6_INTRON/PIK3R3_ENST00000540385.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1227,7 +1227,7 @@ chr1 50679059 rs2480687 G A . PASS FUNCOTATION=[RP11-567C20.3|hg19|chr1|50679059 chr1 51770773 indel.3397 CA C . PASS FUNCOTATION=[TTC39A|hg19|chr1|51770774|51770774|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:51770774delA|ENST00000262676.5|-|8|891|c.729delT|c.(727-729)tttfs|p.F243fs|0.57356608478803|AAAACCCCACAAACTCCAACA|TTC39A_ENST00000447632.2_FRAME_SHIFT_DEL_p.F247fs/TTC39A_ENST00000413473.2_FRAME_SHIFT_DEL_p.F215fs/TTC39A_ENST00000262675.7_FRAME_SHIFT_DEL_p.F184fs/TTC39A_ENST00000371750.5_FRAME_SHIFT_DEL_p.F212fs/TTC39A_ENST00000371747.3_FRAME_SHIFT_DEL_p.F246fs/TTC39A_ENST00000451380.1_FRAME_SHIFT_DEL_p.F211fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 52521798 rs2809954 G T . PASS FUNCOTATION=[TXNDC12|hg19|chr1|52521798|52521798|FIVE_PRIME_UTR||SNP|G|G|T|g.chr1:52521798G>T|ENST00000371626.4|-|1|||||0.5586034912718204|GAGACTGCAAGCCCCAGGATG|BTF3L4_ENST00000313334.8_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 52859335 indel.3466 GA G . PASS FUNCOTATION=[ORC1|hg19|chr1|52859336|52859336|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:52859336delA|ENST00000371568.3|-|6|1081|c.861delT|c.(859-861)tctfs|p.P288fs|0.4463840399002494|TCAGAGCTGGAGACAAGGTTT|ORC1_ENST00000371566.1_FRAME_SHIFT_DEL_p.P288fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 53158510 indel.3481 CTTCCAAATAGTCCA C . PASS FUNCOTATION=[SELRC1|hg19|chr1|53158511|53158524|FRAME_SHIFT_DEL||DEL|TTCCAAATAGTCCA|TTCCAAATAGTCCA|-|g.chr1:53158511_53158524delTTCCAAATAGTCCA|ENST00000371538.3|-|2|176|c.122_135delTGGACTATTTGGAA|c.(121-138)gtggactatttggaagggfs|p.V41fs|0.5289855072463768|TCCGGATCCCTTCCAAATAGTCCACCAGCCGATA|SELRC1_ENST00000486918.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 53158510 indel.3481 CTTCCAAATAGTCCA C . PASS FUNCOTATION=[SELRC1|hg19|chr1|53158511|53158524|FRAME_SHIFT_DEL||DEL|TTCCAAATAGTCCA|TTCCAAATAGTCCA|-|g.chr1:53158511_53158524delTTCCAAATAGTCCA|ENST00000371538.3|-|2|176_189|c.122_135delTGGACTATTTGGAA|c.(121-138)gtggactatttggaagggfs|p.V41fs|0.5289855072463768|TCCGGATCCCTTCCAAATAGTCCACCAGCCGATA|SELRC1_ENST00000486918.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 53163901 indel.3482 TC T . PASS FUNCOTATION=[SELRC1|hg19|chr1|53163902|53163902|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:53163902delC|ENST00000371538.3|-|1|138|c.97delG|c.(97-99)gacfs|p.D33fs|0.6982543640897756|CCGTCCGGGTCCTTCTCGTGG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 53741391 exm60486 A G . PASS FUNCOTATION=[LRP8|hg19|chr1|53741391|53741391|FIVE_PRIME_UTR||SNP|A|A|G|g.chr1:53741391A>G|ENST00000465675.1|-|5|||||0.57356608478803|TCCCATCCCCACACTGGAACT|LRP8_ENST00000347547.2_INTRON/LRP8_ENST00000306052.6_SILENT_p.C306C/LRP8_ENST00000371454.2_SILENT_p.C306C/LRP8_ENST00000354412.3_SILENT_p.C177C|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 54354613 variant.3577 G A . PASS FUNCOTATION=[YIPF1|hg19|chr1|54354613|54354613|FIVE_PRIME_UTR||SNP|G|G|A|g.chr1:54354613G>A|ENST00000072644.1|-|3|||||0.38403990024937656|GCTGCCATTCGGCCAGTGAGT|YIPF1_ENST00000371399.1_INTRON/YIPF1_ENST00000539954.1_NONSENSE_p.R25*/YIPF1_ENST00000469457.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1241,7 +1241,7 @@ chr1 55273582 indel.3699 CT C . PASS FUNCOTATION=[C1orf177|hg19|chr1|55273583|55 chr1 55307523 indel.3707 TA T . PASS FUNCOTATION=[C1orf177|hg19|chr1|55307524|55307524|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:55307524delA|ENST00000371273.3|+|10|1249|c.1235delA|c.(1234-1236)tacfs|p.Y412fs|0.4937655860349127|ACTGTGGATTACAATTCAGAT|C1orf177_ENST00000358193.3_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|LEXM:163747|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|777519771|55307524|false|false|0|false|0|false||false|true|false|DIV|false|0x050000801205000402000200|1|false|144|rs777519771] chr1 57258130 indel.3786 TG T . PASS FUNCOTATION=[C1orf168|hg19|chr1|57258131|57258131|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr1:57258131delG|ENST00000343433.6|-|2|437|c.355delC|c.(355-357)caafs|p.Q119fs|0.456359102244389|ACATTTGATTGAGTCACCTCT|C1orf168_ENST00000484327.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 57351822 indel.3791 GC G . PASS FUNCOTATION=[C8A|hg19|chr1|57351823|57351823|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:57351823delC|ENST00000361249.3|+|7|1174|c.1079delC|c.(1078-1080)gcafs|p.A360fs|0.40648379052369077|ATTGACAAAGCAAAAATGGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 60228226 indel.3843 GGAGT G . PASS FUNCOTATION=[FGGY|hg19|chr1|60228227|60228230|FRAME_SHIFT_DEL||DEL|GAGT|GAGT|-|g.chr1:60228227_60228230delGAGT|ENST00000371218.4|+|17|1882|c.1699_1702delGAGT|c.(1699-1704)gagtatfs|p.E567fs|0.3886138613861386|ACACCAGAAGGAGTATTTGGCGAT|FGGY_ENST00000371212.1_FRAME_SHIFT_DEL_p.E455fs/FGGY_ENST00000303721.7_FRAME_SHIFT_DEL_p.E543fs/FGGY_ENST00000371210.1_FRAME_SHIFT_DEL_p.E244fs/RP4-782L23.2_ENST00000443012.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|FGGY:55277|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|747593219|60228227|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040402000200|1|false|144|rs747593219] +chr1 60228226 indel.3843 GGAGT G . PASS FUNCOTATION=[FGGY|hg19|chr1|60228227|60228230|FRAME_SHIFT_DEL||DEL|GAGT|GAGT|-|g.chr1:60228227_60228230delGAGT|ENST00000371218.4|+|17|1882_1885|c.1699_1702delGAGT|c.(1699-1704)gagtatfs|p.E567fs|0.3886138613861386|ACACCAGAAGGAGTATTTGGCGAT|FGGY_ENST00000371212.1_FRAME_SHIFT_DEL_p.E455fs/FGGY_ENST00000303721.7_FRAME_SHIFT_DEL_p.E543fs/FGGY_ENST00000371210.1_FRAME_SHIFT_DEL_p.E244fs/RP4-782L23.2_ENST00000443012.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|FGGY:55277|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|747593219|60228227|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040402000200|1|false|144|rs747593219] chr1 60228254 exm1845312 T C . PASS FUNCOTATION=[FGGY|hg19|chr1|60228254|60228254|NONSTOP||SNP|T|T|C|g.chr1:60228254T>C|ENST00000371218.4|+|17|1910|c.1726T>C|c.(1726-1728)Tga>Cga|p.*576R|0.3765586034912718|GAATGATGACTGAACAGGGCT|FGGY_ENST00000371212.1_NONSTOP_p.*464R/FGGY_ENST00000303721.7_NONSTOP_p.*552R/FGGY_ENST00000371210.1_NONSTOP_p.*253R/RP4-782L23.2_ENST00000443012.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.9996_%2C_0.0003994_%2C_.|false|false|0||false|false|false|FGGY:55277|false|true|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|true|201875327|60228254|false|false|0|false|0|false|0.999897_%2C_._%2C_0.000103029|false|false|false|SNV|true|0x050000000205040436000100|1|false|137|rs201875327] chr1 60359359 indel.3849 TG T . PASS FUNCOTATION=[CYP2J2|hg19|chr1|60359360|60359360|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr1:60359360delG|ENST00000371204.3|-|9|1517|c.1472delC|c.(1471-1473)ccafs|p.P491fs|0.4513715710723192|GTGACTGACTGGGGAAATGGT|CYP2J2_ENST00000492633.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 60491129 indel.3860 CA C . PASS FUNCOTATION=[C1orf87|hg19|chr1|60491130|60491130|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:60491130delA|ENST00000371201.3|-|8|1179|c.1070delT|c.(1069-1071)ctgfs|p.L357fs|0.3341645885286783|CAGCAGGCTCAGGGTCAGATA|C1orf87_ENST00000450089.2_FRAME_SHIFT_DEL_p.L128fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1251,12 +1251,12 @@ chr1 62586957 indel.3890 GA G . PASS FUNCOTATION=[INADL|hg19|chr1|62586958|62586 chr1 62672471 indel.3900 CT C . PASS FUNCOTATION=[L1TD1|hg19|chr1|62672472|62672472|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:62672472delT|ENST00000498273.1|+|3|466|c.172delT|c.(172-174)ttafs|p.L58fs|0.3516209476309227|GTTTAAGGTCTTAATGGAAAT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 63282434 indel.3957 CA C . PASS FUNCOTATION=[ATG4C|hg19|chr1|63282435|63282435|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:63282435delA|ENST00000317868.4|+|4|556|c.350delA|c.(349-351)cagfs|p.Q117fs|0.371571072319202|AGAACTGGCCAGATGCTCTTG|ATG4C_ENST00000371120.3_FRAME_SHIFT_DEL_p.Q117fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 63300482 indel.3964 CA C . PASS FUNCOTATION=[ATG4C|hg19|chr1|63300483|63300483|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:63300483delA|ENST00000317868.4|+|9|1255|c.1049delA|c.(1048-1050)caafs|p.Q350fs|0.3341645885286783|CATTACTGCCAATCTTTTGTA|ATG4C_ENST00000371120.3_FRAME_SHIFT_DEL_p.Q350fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 63902553 indel.3980 TCC T . PASS FUNCOTATION=[ALG6|hg19|chr1|63902554|63902555|FRAME_SHIFT_DEL||DEL|CC|CC|-|g.chr1:63902554_63902555delCC|ENST00000263440.4|+|14|1600|c.1393_1394delCC|c.(1393-1395)cctfs|p.P465fs|0.35572139303482586|ACTGGATCCTCCTCAGAAACTA|ALG6_ENST00000371108.4_FRAME_SHIFT_DEL_p.P463fs/ALG6_ENST00000494765.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 63999793 indel.3992 CAA C . PASS FUNCOTATION=[EFCAB7|hg19|chr1|63999794|63999795|FRAME_SHIFT_DEL||DEL|AA|AA|-|g.chr1:63999794_63999795delAA|ENST00000371088.4|+|6|956|c.711_712delAA|c.(709-714)gcaaccfs|p.T238fs|0.32587064676616917|TACTGTCAGCAACCAGGAAGTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 64669794 indel.4009 TATAAG T . PASS FUNCOTATION=[UBE2U|hg19|chr1|64669795|64669799|SPLICE_SITE|FRAME_SHIFT_DEL|DEL|ATAAG|ATAAG|-|g.chr1:64669795_64669799delATAAG|ENST00000371076.3|+|1|305|c.62_66delATAAG|c.(61-66)tataagfs|p.Y21fs|0.3654320987654321|GAGAACAATTATAAGGTAAGTACTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 63902553 indel.3980 TCC T . PASS FUNCOTATION=[ALG6|hg19|chr1|63902554|63902555|FRAME_SHIFT_DEL||DEL|CC|CC|-|g.chr1:63902554_63902555delCC|ENST00000263440.4|+|14|1600_1601|c.1393_1394delCC|c.(1393-1395)cctfs|p.P465fs|0.35572139303482586|ACTGGATCCTCCTCAGAAACTA|ALG6_ENST00000371108.4_FRAME_SHIFT_DEL_p.P463fs/ALG6_ENST00000494765.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 63999793 indel.3992 CAA C . PASS FUNCOTATION=[EFCAB7|hg19|chr1|63999794|63999795|FRAME_SHIFT_DEL||DEL|AA|AA|-|g.chr1:63999794_63999795delAA|ENST00000371088.4|+|6|956_957|c.711_712delAA|c.(709-714)gcaaccfs|p.T238fs|0.32587064676616917|TACTGTCAGCAACCAGGAAGTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 64669794 indel.4009 TATAAG T . PASS FUNCOTATION=[UBE2U|hg19|chr1|64669795|64669799|SPLICE_SITE|FRAME_SHIFT_DEL|DEL|ATAAG|ATAAG|-|g.chr1:64669795_64669799delATAAG|ENST00000371076.3|+|1|305_309|c.62_66delATAAG|c.(61-66)tataagfs|p.Y21fs|0.3654320987654321|GAGAACAATTATAAGGTAAGTACTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 64676467 var_1_64676467 AC A . PASS FUNCOTATION=[UBE2U|hg19|chr1|64676468|64676468|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:64676468delC|ENST00000371076.3|+|4|528|c.285delC|c.(283-285)aacfs|p.P96fs|0.30423940149625933|TTTTGGACAACCCTGAGAAGT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 67288063 indel.4057 G GCT . PASS FUNCOTATION=[WDR78|hg19|chr1|67288063|67288064|FRAME_SHIFT_INS||INS|-|-|CT|g.chr1:67288063_67288064insCT|ENST00000371026.3|-|16|2533|c.2476_2477insAG|c.(2476-2478)actfs|p.T826fs|0.3275|TCCAAAACAGTAGGCATATT|WDR78_ENST00000431318.1_FRAME_SHIFT_INS_p.T539fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|WDR78:79819|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|754415129|67288063|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs754415129] -chr1 67474834 indel.4082 TAA T . PASS FUNCOTATION=[SLC35D1|hg19|chr1|67474835|67474836|FRAME_SHIFT_DEL||DEL|AA|AA|-|g.chr1:67474835_67474836delAA|ENST00000235345.5|-|11|979|c.891_892delTT|c.(889-891)actfs|p.I299fs|0.26616915422885573|ATTCCAATATAAGTTATTAATA|SLC35D1_ENST00000506472.2_FRAME_SHIFT_DEL_p.I220fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 67474834 indel.4082 TAA T . PASS FUNCOTATION=[SLC35D1|hg19|chr1|67474835|67474836|FRAME_SHIFT_DEL||DEL|AA|AA|-|g.chr1:67474835_67474836delAA|ENST00000235345.5|-|11|979_980|c.891_892delTT|c.(889-891)actfs|p.I299fs|0.26616915422885573|ATTCCAATATAAGTTATTAATA|SLC35D1_ENST00000506472.2_FRAME_SHIFT_DEL_p.I220fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 67773351 rs12142823 C T . PASS FUNCOTATION=[IL12RB2|hg19|chr1|67773351|67773351|DE_NOVO_START_OUT_FRAME||SNP|C|C|T|g.chr1:67773351C>T|ENST00000262345.1|+|1|||||0.6633416458852868|GTGGAAACCACGGGCGCCCGC|IL12RB2_ENST00000371000.1_DE_NOVO_START_OUT_FRAME|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8325_%2C_._%2C_0.1675|false|false|1||false|true|true|IL12RB2:3595|true|true|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|true|false|12142823|67773351|false|false|0|true|0|false|0.85727_%2C_6.8686e-005_%2C_0.142661|false|false|true|SNV|true|0x05010042000517053e000100|1|false|120|rs12142823] chr1 68564373 indel.4122 TC T . PASS FUNCOTATION=[WLS|hg19|chr1|68564374|68564374|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:68564374delC|ENST00000354777.2|-|12|1820|c.1573delG|c.(1573-1575)gaafs|p.E525fs|0.3341645885286783|CTGAACAATTCTTGATAAAGT|WLS_ENST00000540432.1_FRAME_SHIFT_DEL_p.E527fs/GNG12-AS1_ENST00000420587.1_RNA/GNG12-AS1_ENST00000413628.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 68564392 indel.4123 CA C . PASS FUNCOTATION=[WLS|hg19|chr1|68564393|68564393|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:68564393delA|ENST00000354777.2|-|12|1801|c.1554delT|c.(1552-1554)tttfs|p.F518fs|0.33915211970074816|GTTCCGAAACAAACAAAGCAC|WLS_ENST00000540432.1_FRAME_SHIFT_DEL_p.F520fs/GNG12-AS1_ENST00000420587.1_RNA/GNG12-AS1_ENST00000413628.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1264,8 +1264,8 @@ chr1 70820699 indel.4171 GC G . PASS FUNCOTATION=[HHLA3|hg19|chr1|70820700|70820 chr1 70904381 indel.4182 AC A . PASS FUNCOTATION=[CTH|hg19|chr1|70904382|70904382|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:70904382delC|ENST00000370938.3|+|11|1207|c.1064delC|c.(1063-1065)actfs|p.T355fs|0.38902743142144636|GCAATCATGACTCATGCATCA|CTH_ENST00000346806.2_FRAME_SHIFT_DEL_p.T311fs/CTH_ENST00000411986.2_FRAME_SHIFT_DEL_p.T323fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 71418631 indel.4185 TG T . PASS FUNCOTATION=[PTGER3|hg19|chr1|71418632|71418632|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr1:71418632delG|ENST00000356595.4|-|4|1427|c.1215delC|c.(1213-1215)agcfs|p.S405fs|0.3740648379052369|ACACATTAATGCTGCTCACGA|PTGER3_ENST00000414819.1_THREE_PRIME_UTR/PTGER3_ENST00000370931.3_INTRON/PTGER3_ENST00000460330.1_INTRON/PTGER3_ENST00000370932.2_INTRON/PTGER3_ENST00000351052.5_INTRON/PTGER3_ENST00000354608.5_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 74663709 rs11806946 G A . PASS FUNCOTATION=[LRRIQ3|hg19|chr1|74663709|74663709|FIVE_PRIME_UTR||SNP|G|G|A|g.chr1:74663709G>A|ENST00000370911.3|-|1|||||0.5635910224438903|GCCCTTATGAGTTGGAGACAA|LRRIQ3_ENST00000370909.2_FIVE_PRIME_UTR/LRRIQ3_ENST00000354431.4_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 74737317 indel.4219 TGGAGC T . PASS FUNCOTATION=[FPGT-TNNI3K|hg19|chr1|74737318|74737322|FRAME_SHIFT_DEL||DEL|GGAGC|GGAGC|-|g.chr1:74737318_74737322delGGAGC|ENST00000370899.3|+|7|709|c.673_677delGGAGC|c.(673-678)ggagctfs|p.G225fs|0.3950617283950617|GCTTCACAGTGGAGCTGATATACAG|TNNI3K_ENST00000326637.3_FRAME_SHIFT_DEL_p.G124fs/FPGT-TNNI3K_ENST00000557284.2_FRAME_SHIFT_DEL_p.G238fs/FPGT-TNNI3K_ENST00000370895.1_FRAME_SHIFT_DEL_p.G225fs/TNNI3K_ENST00000370891.2_FRAME_SHIFT_DEL_p.G225fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|TNNI3K:51086_%7C_FPGT-TNNI3K:100526835|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|761357894|74737318|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs761357894] -chr1 74835230 indel.4234 CAG C . PASS FUNCOTATION=[FPGT-TNNI3K|hg19|chr1|74835231|74835232|FRAME_SHIFT_DEL||DEL|AG|AG|-|g.chr1:74835231_74835232delAG|ENST00000370899.3|+|18|1968|c.1932_1933delAG|c.(1930-1935)tcagggfs|p.G646fs|0.43034825870646765|AATACATATCAGGGGGTTCTCT|TNNI3K_ENST00000326637.3_FRAME_SHIFT_DEL_p.G545fs/FPGT-TNNI3K_ENST00000557284.2_FRAME_SHIFT_DEL_p.G659fs/FPGT-TNNI3K_ENST00000370895.1_FRAME_SHIFT_DEL_p.G646fs/TNNI3K_ENST00000370891.2_FRAME_SHIFT_DEL_p.G646fs/RP11-439H8.4_ENST00000415549.2_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|TNNI3K:51086_%7C_FPGT-TNNI3K:100526835|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|748927643|74835231|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs748927643] +chr1 74737317 indel.4219 TGGAGC T . PASS FUNCOTATION=[FPGT-TNNI3K|hg19|chr1|74737318|74737322|FRAME_SHIFT_DEL||DEL|GGAGC|GGAGC|-|g.chr1:74737318_74737322delGGAGC|ENST00000370899.3|+|7|709_713|c.673_677delGGAGC|c.(673-678)ggagctfs|p.G225fs|0.3950617283950617|GCTTCACAGTGGAGCTGATATACAG|TNNI3K_ENST00000326637.3_FRAME_SHIFT_DEL_p.G124fs/FPGT-TNNI3K_ENST00000557284.2_FRAME_SHIFT_DEL_p.G238fs/FPGT-TNNI3K_ENST00000370895.1_FRAME_SHIFT_DEL_p.G225fs/TNNI3K_ENST00000370891.2_FRAME_SHIFT_DEL_p.G225fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|TNNI3K:51086_%7C_FPGT-TNNI3K:100526835|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|761357894|74737318|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs761357894] +chr1 74835230 indel.4234 CAG C . PASS FUNCOTATION=[FPGT-TNNI3K|hg19|chr1|74835231|74835232|FRAME_SHIFT_DEL||DEL|AG|AG|-|g.chr1:74835231_74835232delAG|ENST00000370899.3|+|18|1968_1969|c.1932_1933delAG|c.(1930-1935)tcagggfs|p.G646fs|0.43034825870646765|AATACATATCAGGGGGTTCTCT|TNNI3K_ENST00000326637.3_FRAME_SHIFT_DEL_p.G545fs/FPGT-TNNI3K_ENST00000557284.2_FRAME_SHIFT_DEL_p.G659fs/FPGT-TNNI3K_ENST00000370895.1_FRAME_SHIFT_DEL_p.G646fs/TNNI3K_ENST00000370891.2_FRAME_SHIFT_DEL_p.G646fs/RP11-439H8.4_ENST00000415549.2_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|TNNI3K:51086_%7C_FPGT-TNNI3K:100526835|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|748927643|74835231|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs748927643] chr1 75036872 indel.4252 CT C . PASS FUNCOTATION=[C1orf173|hg19|chr1|75036873|75036873|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:75036873delT|ENST00000326665.5|-|14|4741|c.4521delA|c.(4519-4521)cgafs|p.E1508fs|0.5336658354114713|GTTGCTTCTCTCGGGTTTCAG|C1orf173_ENST00000433746.2_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 75038572 var_1_75038572 TC T . PASS FUNCOTATION=[C1orf173|hg19|chr1|75038573|75038573|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:75038573delC|ENST00000326665.5|-|14|3041|c.2821delG|c.(2821-2823)gatfs|p.D941fs|0.5336658354114713|TCTCCGACATCACTCACAGCC|C1orf173_ENST00000433746.2_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 75198740 kgp9120456 A C . PASS FUNCOTATION=[CRYZ|hg19|chr1|75198740|75198740|FIVE_PRIME_UTR||SNP|A|A|C|g.chr1:75198740A>C|ENST00000417775.1|-|1|||||0.5311720698254364|TCCACCCAGGATGTGCGCCTC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1398,7 +1398,7 @@ chr10 90988034 indel.13572 C CGG . PASS FUNCOTATION=[LIPA|hg19|chr10|90988034|90 chr10 95121241 indel.13733 G GGT . PASS FUNCOTATION=[MYOF|hg19|chr10|95121241|95121242|FRAME_SHIFT_INS||INS|-|-|GT|g.chr10:95121241_95121242insGT|ENST00000359263.4|-|28|2942|c.2941_2942insAC|c.(2941-2943)tctfs|p.S981fs|0.47|ATGTCATAAGACCATGCATC|MYOF_ENST00000358334.5_FRAME_SHIFT_INS_p.S968fs/MYOF_ENST00000371501.4_FRAME_SHIFT_INS_p.S981fs/MYOF_ENST00000371502.4_FRAME_SHIFT_INS_p.S981fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr10 102048159 indel.14208 C CA . PASS FUNCOTATION=[PKD2L1|hg19|chr10|102048159|102048160|FRAME_SHIFT_INS||INS|-|-|A|g.chr10:102048159_102048160insA|ENST00000318222.3|-|16|2795|c.2411_2412insT|c.(2410-2412)aggfs|p.R804fs|0.465|CACTTAACTCCTCTGCAACG|PKD2L1_ENST00000338519.3_FRAME_SHIFT_INS_p.R729fs/PKD2L1_ENST00000353274.3_THREE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr10 102684419 indel.14264 A AT . PASS FUNCOTATION=[FAM178A|hg19|chr10|102684419|102684420|FRAME_SHIFT_INS||INS|-|-|T|g.chr10:102684419_102684420insT|ENST00000238961.4|+|5|2203|c.1661_1662insT|c.(1660-1662)aagfs|p.K554fs|0.4225|CTCCTACAAAGTCTCCCCCT|FAM178A_ENST00000370269.3_FRAME_SHIFT_INS_p.K554fs/FAM178A_ENST00000370271.3_FRAME_SHIFT_INS_p.K554fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr10 120795681 indel.14858 TCTCGGTCTCTTG T . PASS FUNCOTATION=[EIF3A|hg19|chr10|120795682|120795693|IN_FRAME_DEL||DEL|CTCGGTCTCTTG|CTCGGTCTCTTG|-|g.chr10:120795682_120795693delCTCGGTCTCTTG|ENST00000369144.3|-|22|4147|c.4007_4018delCAAGAGACCGAG|c.(4006-4020)tcaagagaccgagaa>taa|p.1336_1340SRDRE>*|0.3859223300970874|CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG|EIF3A_ENST00000541549.1_IN_FRAME_DEL_p.1302_1306SRDRE>*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|EIF3A:8661|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|766037789|120795682|false|false|0|false|0|false||false|false|false|DIV|false|0x050000000005000402000200|1|false|144|rs766037789] +chr10 120795681 indel.14858 TCTCGGTCTCTTG T . PASS FUNCOTATION=[EIF3A|hg19|chr10|120795682|120795693|IN_FRAME_DEL||DEL|CTCGGTCTCTTG|CTCGGTCTCTTG|-|g.chr10:120795682_120795693delCTCGGTCTCTTG|ENST00000369144.3|-|22|4147_4158|c.4007_4018delCAAGAGACCGAG|c.(4006-4020)tcaagagaccgagaa>taa|p.1336_1340SRDRE>*|0.3859223300970874|CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG|EIF3A_ENST00000541549.1_IN_FRAME_DEL_p.1302_1306SRDRE>*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|EIF3A:8661|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|766037789|120795682|false|false|0|false|0|false||false|false|false|DIV|false|0x050000000005000402000200|1|false|144|rs766037789] chr10 121541194 indel.14880 A AG . PASS FUNCOTATION=[INPP5F|hg19|chr10|121541194|121541195|FRAME_SHIFT_INS||INS|-|-|G|g.chr10:121541194_121541195insG|ENST00000361976.2|+|3|392|c.226_227insG|c.(226-228)aaafs|p.K76fs|0.3625|TTGGTGGGCAAACTCCCAGG|INPP5F_ENST00000369081.1_FIVE_PRIME_UTR/INPP5F_ENST00000369083.3_FRAME_SHIFT_INS_p.K76fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr10 124794031 exm862402 G T . PASS FUNCOTATION=[ACADSB|hg19|chr10|124794031|124794031|DE_NOVO_START_OUT_FRAME||SNP|G|G|T|g.chr10:124794031G>T|ENST00000368869.4|+|2|||||0.40648379052369077|AAAGAGTTCAGGTAAGTAAAT|ACADSB_ENST00000358776.4_SPLICE_SITE_p.V68F/ACADSB_ENST00000496730.2_SPLICE_SITE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr11 4664657 rs7925271 C T . PASS FUNCOTATION=[OR51E1|hg19|chr11|4664657|4664657|DE_NOVO_START_OUT_FRAME||SNP|C|C|T|g.chr11:4664657C>T|ENST00000396952.5|+|1|||||0.486284289276808|GTGAATTCCACGCTTAGCAAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1414,7 +1414,7 @@ chr11 78282425 exm944472 G C . PASS FUNCOTATION=[NARS2|hg19|chr11|78282425|78282 chr11 111753117 indel.21284 C CGT . PASS FUNCOTATION=[C11orf1|hg19|chr11|111753117|111753118|FRAME_SHIFT_INS||INS|-|-|GT|g.chr11:111753117_111753118insGT|ENST00000530214.1|+|2|90|c.71_72insGT|c.(70-72)acafs|p.N25fs|0.4425|GTTTCCTCACAAACCCACAC|C11orf1_ENST00000528125.1_FIVE_PRIME_UTR/C11orf1_ENST00000260276.3_FRAME_SHIFT_INS_p.N25fs/C11orf1_ENST00000529270.1_FRAME_SHIFT_INS_p.N65fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr11 113565234 exm956500 G A . PASS FUNCOTATION=[TMPRSS5|hg19|chr11|113565234|113565234|DE_NOVO_START_OUT_FRAME||SNP|G|G|A|g.chr11:113565234G>A|ENST00000536856.1|-|6|||||0.5586034912718204|ACCACCCAGCGTGGCGCTAGC|TMPRSS5_ENST00000299882.5_MISSENSE_p.R251C/TMPRSS5_ENST00000540540.1_DE_NOVO_START_OUT_FRAME/TMPRSS5_ENST00000545579.1_MISSENSE_p.R242C/TMPRSS5_ENST00000538955.1_MISSENSE_p.R207C/TMPRSS5_ENST00000544634.1_INTRON/TMPRSS5_ENST00000544476.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr11 113565260 exm1695050 G A . PASS FUNCOTATION=[TMPRSS5|hg19|chr11|113565260|113565260|DE_NOVO_START_IN_FRAME||SNP|G|G|A|g.chr11:113565260G>A|ENST00000536856.1|-|6|||||0.5760598503740648|GCCCCCACACGTGTGCCGGAA|TMPRSS5_ENST00000299882.5_MISSENSE_p.T242M/TMPRSS5_ENST00000545579.1_MISSENSE_p.T233M/TMPRSS5_ENST00000540540.1_DE_NOVO_START_IN_FRAME/TMPRSS5_ENST00000538955.1_MISSENSE_p.T198M/TMPRSS5_ENST00000544634.1_INTRON/TMPRSS5_ENST00000544476.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr12 11243923 indel.23289 TTTCACC T . PASS FUNCOTATION=[TAS2R43|hg19|chr12|11243924|11243929|IN_FRAME_DEL||DEL|TTCACC|TTCACC|-|g.chr12:11243924_11243929delTTCACC|ENST00000531678.1|-|1|990|c.900_905delGGTGAA|c.(898-906)tgggtgaaa>tga|p.300_302WVK>*|0.35714285714285715|CTTCTCTCCTTTCACCCAGTACCTCA|TAS2R14_ENST00000381852.4_INTRON/PRR4_ENST00000536668.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PRH1-TAS2R14:106707243_%7C_TAS2R43:259289_%7C_PRH1:5554_%7C_PRH1-PRR4:100533464|false|true|true|false|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|867813065|11243924|false|false|0|false|0|false||false|false|false|DIV|false|0x050000080005000402000210|1|false|147|rs867813065] +chr12 11243923 indel.23289 TTTCACC T . PASS FUNCOTATION=[TAS2R43|hg19|chr12|11243924|11243929|IN_FRAME_DEL||DEL|TTCACC|TTCACC|-|g.chr12:11243924_11243929delTTCACC|ENST00000531678.1|-|1|990_995|c.900_905delGGTGAA|c.(898-906)tgggtgaaa>tga|p.300_302WVK>*|0.35714285714285715|CTTCTCTCCTTTCACCCAGTACCTCA|TAS2R14_ENST00000381852.4_INTRON/PRR4_ENST00000536668.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PRH1-TAS2R14:106707243_%7C_TAS2R43:259289_%7C_PRH1:5554_%7C_PRH1-PRR4:100533464|false|true|true|false|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|867813065|11243924|false|false|0|false|0|false||false|false|false|DIV|false|0x050000080005000402000210|1|false|147|rs867813065] chr12 29597130 indel.23912 T TA . PASS FUNCOTATION=[OVCH1|hg19|chr12|29597130|29597131|FRAME_SHIFT_INS||INS|-|-|A|g.chr12:29597130_29597131insA|ENST00000318184.5|-|24|2965|c.2964_2965insT|c.(2965-2967)aagfs|p.K989fs|0.3825|CTTCTGGCTTGGTCAGAAGA|OVCH1-AS1_ENST00000551108.1_INTRON/OVCH1-AS1_ENST00000549411.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr12 52201139 indel.24708 A AC . PASS FUNCOTATION=[SCN8A|hg19|chr12|52201139|52201140|FRAME_SHIFT_INS||INS|-|-|C|g.chr12:52201139_52201140insC|ENST00000354534.6|+|27|6047|c.5869_5870insC|c.(5869-5871)aaafs|p.K1957fs|0.465|GAAAAGGAGAAACAGCAGCG|SCN8A_ENST00000545061.1_FRAME_SHIFT_INS_p.K1916fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr12 53699726 indel.24975 T TA . PASS FUNCOTATION=[C12orf10|hg19|chr12|53699726|53699727|FRAME_SHIFT_INS||INS|-|-|A|g.chr12:53699726_53699727insA|ENST00000549488.1|+|2|205|c.35_36insA|c.(34-36)gtgfs|p.D13fs|0.515|TGGATGCTGTGGACAATGGG|C12orf10_ENST00000267103.5_FRAME_SHIFT_INS_p.D176fs/C12orf10_ENST00000548632.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1582,7 +1582,7 @@ chr5 36227619 exm450129 T C . PASS FUNCOTATION=[NADK2|hg19|chr5|36227619|3622761 chr5 43388500 exm453467 A T . PASS FUNCOTATION=[CCL28|hg19|chr5|43388500|43388500|START_CODON_SNP||SNP|A|A|T|g.chr5:43388500A>T|ENST00000513525.1|-|2|309|c.2T>A|c.(1-3)aTg>aAg|p.M1K|0.4239401496259352|GATGCGACACATATTCACTCT|CCL28_ENST00000361115.4_MISSENSE_p.M48K/CCL28_ENST00000537013.1_MISSENSE_p.M48K|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr5 43656769 indel.84762 G GT . PASS FUNCOTATION=[NNT|hg19|chr5|43656769|43656770|FRAME_SHIFT_INS||INS|-|-|T|g.chr5:43656769_43656770insT|ENST00000264663.5|+|16|2529|c.2308_2309insT|c.(2308-2310)gccfs|p.A770fs|0.415|CTGAAATCTGCCCCTCTCCT|NNT_ENST00000344920.4_FRAME_SHIFT_INS_p.A770fs/NNT_ENST00000512996.2_FRAME_SHIFT_INS_p.A639fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr5 44809066 exm453799 T C . PASS FUNCOTATION=[MRPS30|hg19|chr5|44809066|44809066|START_CODON_SNP||SNP|T|T|C|g.chr5:44809066T>C|ENST00000507110.1|+|1|40|c.2T>C|c.(1-3)aTg>aCg|p.M1T|0.5910224438902744|CGGGCAAAGATGGCGGCGGCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr5 54329752 indel.84832 TAA T . PASS FUNCOTATION=[GZMK|hg19|chr5|54329753|54329754|NONSTOP||DEL|AA|AA|-|g.chr5:54329753_54329754delAA|ENST00000231009.2|+|5|863|c.794_795delAA|c.(793-795)taafs|p.*265fs|0.39800995024875624|CATACAAATTAAGTTACAAATA|CTD-2313F11.1_ENST00000609699.1_RNA/CTD-2313F11.1_ENST00000595218.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr5 54329752 indel.84832 TAA T . PASS FUNCOTATION=[GZMK|hg19|chr5|54329753|54329754|NONSTOP||DEL|AA|AA|-|g.chr5:54329753_54329754delAA|ENST00000231009.2|+|5|863_864|c.794_795delAA|c.(793-795)taafs|p.*265fs|0.39800995024875624|CATACAAATTAAGTTACAAATA|CTD-2313F11.1_ENST00000609699.1_RNA/CTD-2313F11.1_ENST00000595218.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr5 76342200 indel.85335 T TA . PASS FUNCOTATION=[AGGF1|hg19|chr5|76342200|76342201|FRAME_SHIFT_INS||INS|-|-|A|g.chr5:76342200_76342201insA|ENST00000312916.7|+|6|1281|c.899_900insA|c.(898-900)ttcfs|p.F300fs|0.3725|AAAAAGCCTTCAGTGTTGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr5 94785984 exm467542 T C . PASS FUNCOTATION=[FAM81B|hg19|chr5|94785984|94785984|NONSTOP||SNP|T|T|C|g.chr5:94785984T>C|ENST00000283357.5|+|10|1403|c.1357T>C|c.(1357-1359)Taa>Caa|p.*453Q|0.32418952618453867|CCAGGAAGTATAAACCTTTTC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr5 101572564 exm469248 A G . PASS FUNCOTATION=[SLCO4C1|hg19|chr5|101572564|101572564|NONSTOP||SNP|A|A|G|g.chr5:101572564A>G|ENST00000310954.6|-|13|2460|c.2173T>C|c.(2173-2175)Tga>Cga|p.*725R|0.3192019950124688|TTCCCATTTCACCCTTCTTTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1632,7 +1632,7 @@ chr6 49604523 newrs121918588 C A . PASS FUNCOTATION=[RHAG|hg19|chr6|49604523|496 chr6 52285209 exm555450 A G . PASS FUNCOTATION=[EFHC1|hg19|chr6|52285209|52285209|START_CODON_SNP||SNP|A|A|G|g.chr6:52285209A>G|ENST00000371068.5|+|1|104|c.1A>G|c.(1-3)Atg>Gtg|p.M1V|0.6134663341645885|ACCGGCTGCAATGGTGTCCAA|EFHC1_ENST00000433625.2_FIVE_PRIME_UTR/EFHC1_ENST00000491749.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr6 76782204 exm562176 A T . PASS FUNCOTATION=[IMPG1|hg19|chr6|76782204|76782204|START_CODON_SNP||SNP|A|A|T|g.chr6:76782204A>T|ENST00000369950.3|-|1|192|c.2T>A|c.(1-3)aTg>aAg|p.M1K|0.3167082294264339|TTCCAAATACATTCTGGCTTT|IMPG1_ENST00000369963.3_START_CODON_SNP_p.M1K|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr6 84567107 exm563671 A C . PASS FUNCOTATION=[RIPPLY2|hg19|chr6|84567107|84567107|NONSTOP||SNP|A|A|C|g.chr6:84567107A>C|ENST00000369689.1|+|4|537|c.386A>C|c.(385-387)tAa>tCa|p.*129S|0.2793017456359102|TGTGAAAATTAATCTGATTAG|RIPPLY2_ENST00000369687.1_NONSTOP_p.*71S|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr6 88255394 var_6_88255394 CTTT C . PASS FUNCOTATION=[RARS2|hg19|chr6|88255395|88255397|IN_FRAME_DEL||DEL|TTT|TTT|-|g.chr6:88255395_88255397delTTT|ENST00000369536.5|-|7|521|c.472_474delAAA|c.(472-474)aaadel|p.K158del|0.2903225806451613|CTAAAGCTTCTTTGAGATTTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|RARS2:57038|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|757743894|88255395|false|false|0|false|0|false|0.999966_%2C_3.4343e-005|false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs757743894] +chr6 88255394 var_6_88255394 CTTT C . PASS FUNCOTATION=[RARS2|hg19|chr6|88255395|88255397|IN_FRAME_DEL||DEL|TTT|TTT|-|g.chr6:88255395_88255397delTTT|ENST00000369536.5|-|7|521_523|c.472_474delAAA|c.(472-474)aaadel|p.K158del|0.2903225806451613|CTAAAGCTTCTTTGAGATTTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|RARS2:57038|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|757743894|88255395|false|false|0|false|0|false|0.999966_%2C_3.4343e-005|false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs757743894] chr6 109954114 exm571178 T A . PASS FUNCOTATION=[AK9|hg19|chr6|109954114|109954114|NONSTOP||SNP|T|T|A|g.chr6:109954114T>A|ENST00000285397.5|-|12|1348|c.1266A>T|c.(1264-1266)taA>taT|p.*422Y|0.33915211970074816|AGACAGATAGTTAGTTAGTCA|AK9_ENST00000368948.2_INTRON/AK9_ENST00000424296.2_INTRON/AK9_ENST00000341338.6_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr6 117249986 indel.92725 C CA . PASS FUNCOTATION=[RFX6|hg19|chr6|117249986|117249987|FRAME_SHIFT_INS||INS|-|-|A|g.chr6:117249986_117249987insA|ENST00000332958.2|+|18|2479|c.2463_2464insA|c.(2464-2466)gttfs|p.V822fs|0.3925|GAATCAGCACGTTTCTGTCA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr6 132874859 exm579084 A G . PASS FUNCOTATION=[TAAR8|hg19|chr6|132874859|132874859|SPLICE_SITE|SILENT|SNP|A|A|G|g.chr6:132874859A>G|ENST00000275200.1|+|1|1028|c.1028A>G|c.(1027-1029)tAa>tGa|p.*343*|0.26184538653366585|TTTTTAGAATAAGTTTAAGCA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] @@ -1646,7 +1646,7 @@ chr6 166308924 rs10806835 G A . PASS FUNCOTATION=[SDIM1|hg19|chr6|166308924|1663 chr7 20685486 indel.94825 G GA . PASS FUNCOTATION=[ABCB5|hg19|chr7|20685486|20685487|FRAME_SHIFT_INS||INS|-|-|A|g.chr7:20685486_20685487insA|ENST00000404938.2|+|8|1438|c.786_787insA|c.(787-789)gagfs|p.E263fs|0.3725|TAGGGCCCAGGAGAAAGAAC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr7 23338972 exm609536 A G . PASS FUNCOTATION=[MALSU1|hg19|chr7|23338972|23338972|START_CODON_SNP||SNP|A|A|G|g.chr7:23338972A>G|ENST00000466681.1|+|1|154|c.1A>G|c.(1-3)Atg>Gtg|p.M1V|0.6708229426433915|GGCTGCTGCTATGGGGCCGGG|MALSU1_ENST00000479974.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr7 23749905 exm609783 A T . PASS FUNCOTATION=[STK31|hg19|chr7|23749905|23749905|START_CODON_SNP||SNP|A|A|T|g.chr7:23749905A>T|ENST00000355870.3|+|1|120|c.1A>T|c.(1-3)Atg>Ttg|p.M1L|0.6234413965087282|AAAGTCCAGTATGTGGGTCCA|STK31_ENST00000433467.2_START_CODON_SNP_p.M1L|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr7 27181455 indel.95055 CAG C . PASS FUNCOTATION=[HOXA5|hg19|chr7|27181456|27181457|NONSTOP||DEL|AG|AG|-|g.chr7:27181456_27181457delAG|ENST00000222726.3|-|2|873|c.810_811delCT|c.(808-810)cccfs|p.*271fs|0.4651741293532338|TCAGATACTCAGGGACGGAAGG|RP1-170O19.22_ENST00000467897.2_RNA/HOXA-AS3_ENST00000521197.1_RNA/HOXA-AS3_ENST00000518848.1_RNA/HOXA5_ENST00000520854.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr7 27181455 indel.95055 CAG C . PASS FUNCOTATION=[HOXA5|hg19|chr7|27181456|27181457|NONSTOP||DEL|AG|AG|-|g.chr7:27181456_27181457delAG|ENST00000222726.3|-|2|873_874|c.810_811delCT|c.(808-810)cccfs|p.*271fs|0.4651741293532338|TCAGATACTCAGGGACGGAAGG|RP1-170O19.22_ENST00000467897.2_RNA/HOXA-AS3_ENST00000521197.1_RNA/HOXA-AS3_ENST00000518848.1_RNA/HOXA5_ENST00000520854.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr7 33134847 var_7_33134847 CA C . PASS FUNCOTATION=[RP9|hg19|chr7|33134848|33134848|NONSTOP||DEL|A|A|-|g.chr7:33134848delA|ENST00000297157.3|-|6|683|c.664delT|c.(664-666)tgafs|p.*222fs|0.4488778054862843|CATCCTTGTCACTCTGAGTCA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr7 48278997 indel.95654 C CGGTA . PASS FUNCOTATION=[ABCA13|hg19|chr7|48278997|48278998|FRAME_SHIFT_INS||INS|-|-|GGTA|g.chr7:48278997_48278998insGGTA|ENST00000435803.1|+|9|1081|c.1057_1058insGGTA|c.(1057-1059)caafs|p.Q353fs|0.495|CGAGTCTACCAACAGGTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr7 54610426 exm621856 G A . PASS FUNCOTATION=[VSTM2A|hg19|chr7|54610426|54610426|START_CODON_SNP||SNP|G|G|A|g.chr7:54610426G>A|ENST00000404951.1|+|1|318|c.3G>A|c.(1-3)atG>atA|p.M1I|0.4837905236907731|TTTTTGGAATGATGGGGATCT|VSTM2A_ENST00000407838.3_START_CODON_SNP_p.M1I/VSTM2A_ENST00000302287.3_START_CODON_SNP_p.M1I/VSTM2A_ENST00000402613.3_START_CODON_SNP_p.M1I/VSTM2A_ENST00000402026.2_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.maf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.maf index 848b5453480..78f3339e9b4 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.maf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.maf @@ -88,9 +88,9 @@ ## contig= ## contig= ## contig= -## GATKCommandLine= ## source=Funcotator -## Funcotator 0.0.5 | Date 20184130T024117 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 +## GATKCommandLine= +## Funcotator 0.0.5 | Date 20184831T034814 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_19_secondaryVariantClassification Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_ASSEMBLY ClinVar_rs CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Simple_Uniprot_alt_uniprot_accessions dbSNP_AC dbSNP_AF dbSNP_AN dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DP dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD RP11-206L10.10 __UNKNOWN__ hg19 1 752566 752566 + RNA SNP G G A 3094315 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:752566G>A ENST00000435300.1 - c.e1-187C>T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGAGAAACGTTTGACAGAG 0.3690773067331671 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.2817,0.7183 false false 1 false true false FAM87B:400728 true true false true true false false false false false false false false false false true true false true false true false 0 true 0 false 0.351947,0.648053 false false false SNV 0x05012802000515053f000101 1 false 103 rs3094315 752566 true RP11-206L10.10 __UNKNOWN__ hg19 1 752721 752721 + RNA SNP A A G 3131972 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:752721A>G ENST00000435300.1 - c.e1-32T>C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAAGGAAAAGGGAAGAATG 0.486284289276808 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.3466,0.6534 false false 1 false true true FAM87B:400728 true true false true true false false false false false false false false false false false false false true false true false 0 true 0 false 0.393296,0.606704 false false false SNV 0x05010002000517053f000100 1 false 103 rs3131972 752721 true @@ -189,11 +189,11 @@ PLEKHG5 __UNKNOWN__ hg19 1 6556585 6556585 + Missense_Mutation SNP G G A 201669 TAS1R1 __UNKNOWN__ hg19 1 6635346 6635347 + Frame_Shift_Del DEL C C - 867182312 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:6635346delC ENST00000333172.6 + 3 1346 c.1154delC c.(1153-1155)tctfs p.S385fs TAS1R1_ENST00000351136.3_Intron|TAS1R1_ENST00000328191.4_Frame_Shift_Del_p.S385fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCATGAGTTCTGCCTACAAC 0.600997506234414 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false TAS1R1:80835 false true true false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000081205000402000200 1 false 147 rs867182312 6635346 false PER3 __UNKNOWN__ hg19 1 7897139 7897140 + Frame_Shift_Del DEL A A - 773961726 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:7897139delA ENST00000377532.3 + 20 3702 c.3479delA c.(3478-3480)caafs p.K1161fs PER3_ENST00000361923.2_Frame_Shift_Del_p.K1152fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTCATGGGCAAAAGGAGGAG 0.3940149625935162 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PER3:8863 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs773961726 7897139 false UTS2 __UNKNOWN__ hg19 1 7913430 7913430 + DE_NOVO_START_IN_FRAME SNP G G A 228648 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:7913430G>A ENST00000377516.2 - 1 UTS2_ENST00000054668.5_Missense_Mutation_p.T21M __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCAAAGAGACGTGGATTTATG 0.3566084788029925 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.5216,0.4784 false false 1 false true true UTS2:10911 true true false true true false false false false false false true false false false true true false true true false false 0 true 0 false 0.476578,0.523422 false false false SNV 0x050128020a0517053f000101 1 false 79 rs228648 7913430 true -PARK7 __UNKNOWN__ hg19 1 8045015 8045020 + In_Frame_Del DEL GCC GCC - 764877312 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8045015_8045017delGCC ENST00000493678.1 + 7 537 c.471_473delGCC c.(469-474)gggcct>ggt p.P158del PARK7_ENST00000377491.1_In_Frame_Del_p.P158del|PARK7_ENST00000338639.5_In_Frame_Del_p.P158del|PARK7_ENST00000377488.1_In_Frame_Del_p.P158del|PARK7_ENST00000377493.5_In_Frame_Del_p.P138del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGCCGGGGGCCTGGGACCAGC 0.4466501240694789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PARK7:11315 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005040402000200 1 false 144 rs764877312 8045015 true +PARK7 __UNKNOWN__ hg19 1 8045015 8045020 + In_Frame_Del DEL GCC GCC - 764877312 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:8045015_8045017delGCC ENST00000493678.1 + 7 537_539 c.471_473delGCC c.(469-474)gggcct>ggt p.P158del PARK7_ENST00000377491.1_In_Frame_Del_p.P158del|PARK7_ENST00000338639.5_In_Frame_Del_p.P158del|PARK7_ENST00000377488.1_In_Frame_Del_p.P158del|PARK7_ENST00000377493.5_In_Frame_Del_p.P138del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGCCGGGGGCCTGGGACCAGC 0.4466501240694789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PARK7:11315 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005040402000200 1 false 144 rs764877312 8045015 true LZIC __UNKNOWN__ hg19 1 9994823 9994824 + Frame_Shift_Del DEL T T - 866608629 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:9994823delT ENST00000377223.1 - 5 582 c.333delA c.(331-333)gcafs p.E112fs LZIC_ENST00000377213.1_Frame_Shift_Del_p.E112fs|LZIC_ENST00000400903.2_Frame_Shift_Del_p.E112fs|LZIC_ENST00000541052.1_Frame_Shift_Del_p.E133fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATTTTACCTCTGCTAACCTTG 0.3516209476309227 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false LZIC:84328 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 147 rs866608629 9994823 false PGD __UNKNOWN__ hg19 1 10478955 10478956 + Frame_Shift_Del DEL C C - 767877628 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:10478955delC ENST00000270776.8 + 11 1219 c.1182delC c.(1180-1182)ttcfs p.F395fs PGD_ENST00000538557.1_Frame_Shift_Del_p.F382fs|PGD_ENST00000541529.1_Frame_Shift_Del_p.F373fs|PGD_ENST00000498356.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGGACGACTTCTTTAAGTCAG 0.46384039900249374 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PGD:5226 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs767877628 10478955 false NPPA __UNKNOWN__ hg19 1 11906068 11906068 + Nonstop_Mutation SNP A A G 5065 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:11906068A>G ENST00000376480.3 - 3 553 c.454T>C c.(454-456)Tga>Cga p.*152R NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA-AS1_ENST00000446542.1_RNA|NPPA-AS1_ENST00000400892.2_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGTTATCTTCAGTACTGCAAA 0.4937655860349127 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8209,0.1791 false false 1 false true false NPPA:4878|NPPA-AS1:100379251 true true true true true false false false false false false false false false false true true false false true false false 0 true 0 false 0.737688,0.262312 true false false SNV 0x05013808020515053f000100 1 false 52 rs5065 11906068 true -MFN2 __UNKNOWN__ hg19 1 12069757 12069764 + Frame_Shift_Del DEL ACTT ACTT - 772270096 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12069757_12069760delACTT ENST00000235329.5 + 18 2499 c.2178_2181delACTT c.(2176-2181)tcacttfs p.L727fs MFN2_ENST00000444836.1_Frame_Shift_Del_p.L727fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCTTGACTCACTTCAGAGCAAAG 0.5693069306930693 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false MFN2:9927 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs772270096 12069757 false +MFN2 __UNKNOWN__ hg19 1 12069757 12069764 + Frame_Shift_Del DEL ACTT ACTT - 772270096 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12069757_12069760delACTT ENST00000235329.5 + 18 2499_2502 c.2178_2181delACTT c.(2176-2181)tcacttfs p.L727fs MFN2_ENST00000444836.1_Frame_Shift_Del_p.L727fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCTTGACTCACTTCAGAGCAAAG 0.5693069306930693 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false MFN2:9927 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000402000200 1 false 144 rs772270096 12069757 false AADACL3 __UNKNOWN__ hg19 1 12776344 12776344 + 5'UTR SNP A A T 3000859 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:12776344A>T ENST00000359318.5 + 1 AADACL3_ENST00000332530.3_START_CODON_SNP_p.M1L __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGCTGTTGACATGGGTGAGTT 0.5311720698254364 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.3435,0.6565 false false 1 false true true AADACL3:126767 true true false true true false false false false false false true false false false false false false false true true true 0 true 0 true false false false SNV 0x050300000b0517053f000100 1 false 101 rs3000859 12776344 true PDPN __UNKNOWN__ hg19 1 13933727 13933727 + Missense_Mutation SNP A A G 141726617 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:13933727A>G ENST00000509009.1 + 2 156 c.112A>G c.(112-114)Atg>Gtg p.M38V PDPN_ENST00000294489.6_Missense_Mutation_p.M119V|PDPN_ENST00000376057.4_Missense_Mutation_p.M119V|PDPN_ENST00000376061.4_START_CODON_SNP_p.M1V|PDPN_ENST00000513143.1_START_CODON_SNP_p.M1V|PDPN_ENST00000475043.1_START_CODON_SNP_p.M1V|PDPN_ENST00000487038.1_START_CODON_SNP_p.M1V __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGCGTTGCCATGCCAGGTGC 0.42144638403990026 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.9954,0.004593 false false 1 false false false PDPN:10630 false true false true true false false false false false false true false false false false false false false true false false 0 false 0 false 0.990487,0.00951302 false false false SNV 0x050000000a05040436000100 1 false 134 rs141726617 13933727 true FHAD1 __UNKNOWN__ hg19 1 15671649 15671649 + Missense_Mutation SNP T T C 200826682 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:15671649T>C ENST00000375998.4 + 15 2135 c.2135T>C c.(2134-2136)aTg>aCg p.M712T FHAD1_ENST00000358897.4_Missense_Mutation_p.M712T|FHAD1_ENST00000417793.1_Missense_Mutation_p.M712T|FHAD1_ENST00000375999.3_Missense_Mutation_p.M712T|FHAD1_ENST00000314740.8_START_CODON_SNP_p.M1T|FHAD1_ENST00000471347.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGAAGAGAATGCAAGAACTG 0.571072319201995 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false FHAD1:114827|LOC101927417:101927417 false true false false false false false false false false false true false false false false false false true true false false 0 false 0 false 0.999554,0.000446459 false false false SNV 0x050000020a05040402000100 1 false 137 rs200826682 15671649 true @@ -247,45 +247,45 @@ PIK3CA __UNKNOWN__ hg19 3 178936089 178936090 + Frame_Shift_Ins INS - - GT __ PIK3CA __UNKNOWN__ hg19 3 178936089 178936090 + In_Frame_Ins INS - - GTC __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936089_178936090insGTC ENST00000263967.3 + 10 1788 c.1631_1632insGTC c.(1630-1632)act>acGTCt p.544_545insS __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAG 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936089 178936090 + Frame_Shift_Ins INS - - GTCG __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936089_178936090insGTCG ENST00000263967.3 + 10 1788 c.1631_1632insGTCG c.(1630-1632)actfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAG 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090delT ENST00000263967.3 + 10 1788 c.1632delT c.(1630-1632)actfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGA 0.29925187032418954 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936090 178936093 + Frame_Shift_Del DEL TG TG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091delTG ENST00000263967.3 + 10 1788 c.1632_1633delTG c.(1630-1635)actgagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAA 0.29850746268656714 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936090 178936095 + In_Frame_Del DEL TGA TGA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936092delTGA ENST00000263967.3 + 10 1788 c.1632_1634delTGA c.(1630-1635)actgag>acg p.E545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAA 0.2977667493796526 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936090 178936097 + Frame_Shift_Del DEL TGAG TGAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936093delTGAG ENST00000263967.3 + 10 1788 c.1632_1635delTGAG c.(1630-1635)actgagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAG 0.2995049504950495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936090 178936101 + In_Frame_Del DEL TGAGCA TGAGCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936095delTGAGCA ENST00000263967.3 + 10 1788 c.1632_1637delTGAGCA c.(1630-1638)actgagcag>acg p.EQ545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAGAT 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936090 178936107 + In_Frame_Del DEL TGAGCAGGA TGAGCAGGA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936098delTGAGCAGGA ENST00000263967.3 + 10 1788 c.1632_1640delTGAGCAGGA c.(1630-1641)actgagcaggag>acg p.EQE545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAGATTTT 0.29584352078239606 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936089 178936094 + Missense_Mutation ONP CTGAGC CTGAGC CGTCCA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936089_178936094CTGAGC>CGTCCA ENST00000263967.3 + 10 1788 c.1631_1636CTGAGC>CGTCCA c.(1630-1638)acTGAGCag>acGTCCAag p.545_546EQ>SK __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTGAAATCACTGAGCAGGAGAAAGA 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936090 178936093 + Frame_Shift_Del DEL TG TG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091delTG ENST00000263967.3 + 10 1788_1789 c.1632_1633delTG c.(1630-1635)actgagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAA 0.29850746268656714 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936090 178936095 + In_Frame_Del DEL TGA TGA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936092delTGA ENST00000263967.3 + 10 1788_1790 c.1632_1634delTGA c.(1630-1635)actgag>acg p.E545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAA 0.2977667493796526 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936090 178936097 + Frame_Shift_Del DEL TGAG TGAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936093delTGAG ENST00000263967.3 + 10 1788_1791 c.1632_1635delTGAG c.(1630-1635)actgagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAG 0.2995049504950495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936090 178936101 + In_Frame_Del DEL TGAGCA TGAGCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936095delTGAGCA ENST00000263967.3 + 10 1788_1793 c.1632_1637delTGAGCA c.(1630-1638)actgagcag>acg p.EQ545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAGAT 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936090 178936107 + In_Frame_Del DEL TGAGCAGGA TGAGCAGGA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936098delTGAGCAGGA ENST00000263967.3 + 10 1788_1796 c.1632_1640delTGAGCAGGA c.(1630-1641)actgagcaggag>acg p.EQE545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGAAATCACTGAGCAGGAGAAAGATTTT 0.29584352078239606 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936089 178936094 + Missense_Mutation ONP CTGAGC CTGAGC CGTCCA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936089_178936094CTGAGC>CGTCCA ENST00000263967.3 + 10 1788_1793 c.1631_1636CTGAGC>CGTCCA c.(1630-1638)acTGAGCag>acGTCCAag p.545_546EQ>SK __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTGAAATCACTGAGCAGGAGAAAGA 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091insA ENST00000263967.3 + 10 1789 c.1632_1633insA c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGA 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + Frame_Shift_Ins INS - - AT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091insAT ENST00000263967.3 + 10 1789 c.1632_1633insAT c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGA 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + In_Frame_Ins INS - - ATT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091insATT ENST00000263967.3 + 10 1789 c.1632_1633insATT c.(1633-1635)gag>ATTgag p.544_545insI __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGA 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + Frame_Shift_Ins INS - - ATTG __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936090_178936091insATTG ENST00000263967.3 + 10 1789 c.1632_1633insATTG c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGA 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936091 178936092 + Frame_Shift_Del DEL G G - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091delG ENST00000263967.3 + 10 1789 c.1633delG c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAA 0.29925187032418954 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936091 178936094 + Frame_Shift_Del DEL GA GA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936092delGA ENST00000263967.3 + 10 1789 c.1633_1634delGA c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAA 0.29850746268656714 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936091 178936096 + In_Frame_Del DEL GAG GAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936093delGAG ENST00000263967.3 + 10 1789 c.1633_1635delGAG c.(1633-1635)gagdel p.E545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAAG 0.3002481389578164 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PIK3CA __UNKNOWN__ hg19 3 178936091 178936098 + Frame_Shift_Del DEL GAGC GAGC - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 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c.1633_1638delGAGCAG c.(1633-1638)gagcagdel p.EQ545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAAGATT 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936091 178936094 + Frame_Shift_Del DEL GA GA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936092delGA ENST00000263967.3 + 10 1789_1790 c.1633_1634delGA c.(1633-1635)gagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAA 0.29850746268656714 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936091 178936096 + In_Frame_Del DEL GAG GAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936093delGAG ENST00000263967.3 + 10 1789_1791 c.1633_1635delGAG c.(1633-1635)gagdel p.E545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAAG 0.3002481389578164 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936091 178936098 + Frame_Shift_Del DEL GAGC GAGC - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936094delGAGC ENST00000263967.3 + 10 1789_1792 c.1633_1636delGAGC c.(1633-1638)gagcagfs p.E545fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAAGA 0.2995049504950495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PIK3CA __UNKNOWN__ hg19 3 178936091 178936102 + In_Frame_Del DEL GAGCAG GAGCAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr3:178936091_178936096delGAGCAG ENST00000263967.3 + 10 1789_1794 c.1633_1638delGAGCAG c.(1633-1638)gagcagdel p.EQ545del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGAAAGATT 0.29802955665024633 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PIK3CA __UNKNOWN__ hg19 3 178936090 178936091 + In_Frame_Ins INS - - GAG __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 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c.1632_1633insGAGC c.(1633-1635)gagfs p.Q546fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGAAATCACTGAGCAGGAGA 0.3 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PRKG2 __UNKNOWN__ hg19 4 82126215 82126215 + Splice_Site SNP C C A 866277244 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr4:82126215C>A ENST00000395578.1 - c.e2+1G>T c.e2-1 PRKG2_ENST00000264399.1_DE_NOVO_START_IN_FRAME|PRKG2_ENST00000418486.2_Splice_Site __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 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__UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr5:1882759_1882760insAT ENST00000505790.1 - 2 460 c.2_3insAT IRX4_ENST00000231357.2_START_CODON_INS_|IRX4_ENST00000513692.1_START_CODON_INS_ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGGTAGGACATGGCGGGCG 0.72 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -RARS2 __UNKNOWN__ hg19 6 88255395 88255400 + In_Frame_Del DEL TTT TTT - 757743894 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:88255395_88255397delTTT ENST00000369536.5 - 7 521 c.472_474delAAA c.(472-474)aaadel p.K158del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTAAAGCTTCTTTGAGATTTGCT 0.2903225806451613 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false RARS2:57038 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false 0.999966,3.4343e-005 false false false DIV 0x050000000005040402000200 1 false 144 rs757743894 88255395 true -EIF3A __UNKNOWN__ hg19 10 120795682 120795705 + In_Frame_Del DEL CTCGGTCTCTTG CTCGGTCTCTTG - 766037789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:120795682_120795693delCTCGGTCTCTTG ENST00000369144.3 - 22 4147 c.4007_4018delCAAGAGACCGAG c.(4006-4020)tcaagagaccgagaa>taa p.1336_1340SRDRE>* EIF3A_ENST00000541549.1_In_Frame_Del_p.1302_1306SRDRE>* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG 0.3859223300970874 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false EIF3A:8661 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005000402000200 1 false 144 rs766037789 120795682 false -TAS2R43 __UNKNOWN__ hg19 12 11243924 11243935 + In_Frame_Del DEL TTCACC TTCACC - 867813065 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:11243924_11243929delTTCACC ENST00000531678.1 - 1 990 c.900_905delGGTGAA c.(898-906)tgggtgaaa>tga p.300_302WVK>* TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTTCTCTCCTTTCACCCAGTACCTCA 0.35714285714285715 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PRH1-TAS2R14:106707243|TAS2R43:259289|PRH1:5554|PRH1-PRR4:100533464 false true true false false false false false true false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000080005000402000210 1 false 147 rs867813065 11243924 false +RARS2 __UNKNOWN__ hg19 6 88255395 88255400 + In_Frame_Del DEL TTT TTT - 757743894 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr6:88255395_88255397delTTT ENST00000369536.5 - 7 521_523 c.472_474delAAA c.(472-474)aaadel p.K158del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTAAAGCTTCTTTGAGATTTGCT 0.2903225806451613 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false RARS2:57038 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false 0.999966,3.4343e-005 false false false DIV 0x050000000005040402000200 1 false 144 rs757743894 88255395 true +EIF3A __UNKNOWN__ hg19 10 120795682 120795705 + In_Frame_Del DEL CTCGGTCTCTTG CTCGGTCTCTTG - 766037789 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr10:120795682_120795693delCTCGGTCTCTTG ENST00000369144.3 - 22 4147_4158 c.4007_4018delCAAGAGACCGAG c.(4006-4020)tcaagagaccgagaa>taa p.1336_1340SRDRE>* EIF3A_ENST00000541549.1_In_Frame_Del_p.1302_1306SRDRE>* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG 0.3859223300970874 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false EIF3A:8661 false true false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005000402000200 1 false 144 rs766037789 120795682 false +TAS2R43 __UNKNOWN__ hg19 12 11243924 11243935 + In_Frame_Del DEL TTCACC TTCACC - 867813065 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:11243924_11243929delTTCACC ENST00000531678.1 - 1 990_995 c.900_905delGGTGAA c.(898-906)tgggtgaaa>tga p.300_302WVK>* TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTTCTCTCCTTTCACCCAGTACCTCA 0.35714285714285715 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false PRH1-TAS2R14:106707243|TAS2R43:259289|PRH1:5554|PRH1-PRR4:100533464 false true true false false false false false true false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000080005000402000210 1 false 147 rs867813065 11243924 false OR6C76 __UNKNOWN__ hg19 12 55820041 55820042 + Frame_Shift_Del DEL A A - 768848732 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr12:55820041delA ENST00000328314.3 + 1 3 c.4delA c.(4-6)aaafs p.N3fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATCAGAAATGAAAAATAGAAC 0.341645885286783 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false OR6C76:390326 false true false false false false false false false false true false false false false false false false false true false false 0 false 0 false 0.999966,3.4343e-005 false false false DIV 0x050000001205000402000200 1 false 144 rs768848732 55820041 false Unknown __UNKNOWN__ hg19 13 60738150 60738150 + IGR SNP C C A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr13:60738150C>A no_transcript __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCCTTCCGGGCACTGCGAAAC 0.6234413965087282 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown __UNKNOWN__ hg19 13 60738151 60738154 + IGR DEL AC AC - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr13:60738151_60738152delAC no_transcript __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTTCCGGGCACTGCGAAACAT 0.6218905472636815 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown __UNKNOWN__ hg19 13 60738150 60738151 + IGR INS - - AC __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr13:60738150_60738151insAC no_transcript __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTTCCGGGCACTGCGAAAC 0.6225 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091787 9091788 + In_Frame_Ins INS - - TTT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091787_9091788insTTT ENST00000397910.4 - 1 232 c.27_28insAAA c.(25-30)gggtca>gggAAAtca p.9_10insK __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGATGACCCAGGAAGG 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091787 9091788 + In_Frame_Ins INS - - TTTTTT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091787_9091788insTTTTTT ENST00000397910.4 - 1 232 c.27_28insAAAAAA c.(25-30)gggtca>gggAAAAAAtca p.9_10insKK __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGATGACCCAGGAAGG 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -MUC16 __UNKNOWN__ hg19 19 9091788 9091795 + Frame_Shift_Del DEL CCCA CCCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091788_9091791delCCCA ENST00000397910.4 - 1 232 c.24_27delTGGG c.(22-27)cctgggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGATGACCCAGGAAGGCCTG 0.5247524752475248 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -MUC16 __UNKNOWN__ hg19 19 9091789 9091794 + In_Frame_Del DEL CCA CCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091791delCCA ENST00000397910.4 - 1 231 c.24_26delTGG c.(22-27)cctggg>ccg p.G9del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGCCTG 0.5235732009925558 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +MUC16 __UNKNOWN__ hg19 19 9091788 9091795 + Frame_Shift_Del DEL CCCA CCCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091788_9091791delCCCA ENST00000397910.4 - 1 232_235 c.24_27delTGGG c.(22-27)cctgggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGAAGATGACCCAGGAAGGCCTG 0.5247524752475248 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +MUC16 __UNKNOWN__ hg19 19 9091789 9091794 + In_Frame_Del DEL CCA CCA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091791delCCA ENST00000397910.4 - 1 231_233 c.24_26delTGG c.(22-27)cctggg>ccg p.G9del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGCCTG 0.5235732009925558 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091788 9091789 + In_Frame_Ins INS - - TAA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091788_9091789insTAA ENST00000397910.4 - 1 231 c.26_27insTTA c.(25-27)ggg>ggTTAg p.9_10ins* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091788 9091789 + In_Frame_Ins INS - - TAATAA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091788_9091789insTAATAA ENST00000397910.4 - 1 231 c.26_27insTTATTA c.(25-27)ggg>ggTTATTAg p.9_10insY* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -MUC16 __UNKNOWN__ hg19 19 9091790 9091793 + Frame_Shift_Del DEL CA CA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091790_9091791delCA ENST00000397910.4 - 1 230 c.24_25delTG c.(22-24)cctfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCCTG 0.5248756218905473 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +MUC16 __UNKNOWN__ hg19 19 9091790 9091793 + Frame_Shift_Del DEL CA CA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091790_9091791delCA ENST00000397910.4 - 1 230_231 c.24_25delTG c.(22-24)cctfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCCTG 0.5248756218905473 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091789 9091790 + Frame_Shift_Ins INS - - T __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091790insT ENST00000397910.4 - 1 230 c.25_26insA c.(25-27)gggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091789 9091790 + Frame_Shift_Ins INS - - TA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091790insTA ENST00000397910.4 - 1 230 c.25_26insTA c.(25-27)gggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091789 9091790 + In_Frame_Ins INS - - TAA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091790insTAA ENST00000397910.4 - 1 230 c.25_26insTTA c.(25-27)ggg>gTTAgg p.G9VR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091789 9091790 + In_Frame_Ins INS - - TAATAA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091790insTAATAA ENST00000397910.4 - 1 230 c.25_26insTTATTA c.(25-27)ggg>gTTATTAgg p.G9VIR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAAGATGACCCAGGAAGGCC 0.5275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -MUC16 __UNKNOWN__ hg19 19 9091789 9091794 + Missense_Mutation ONP CCAGGA CCAGGA CGTCCT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091794CCAGGA>CGTCCT ENST00000397910.4 - 1 230 c.21_26TCCTGG>AGGACG c.(19-27)ctTCCTGgg>ctAGGACgg p.8_9PG>GR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGCCTGAGG 0.5246305418719212 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +MUC16 __UNKNOWN__ hg19 19 9091789 9091794 + Missense_Mutation ONP CCAGGA CCAGGA CGTCCT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091789_9091794CCAGGA>CGTCCT ENST00000397910.4 - 1 230_235 c.21_26TCCTGG>AGGACG c.(19-27)ctTCCTGgg>ctAGGACgg p.8_9PG>GR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGAAGATGACCCAGGAAGGCCTGAGG 0.5246305418719212 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091790 9091791 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091790_9091791insA ENST00000397910.4 - 1 229 c.24_25insT c.(25-27)gggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAGATGACCCAGGAAGGCCT 0.525 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091790 9091791 + Frame_Shift_Ins INS - - AT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091790_9091791insAT ENST00000397910.4 - 1 229 c.24_25insAT c.(25-27)gggfs p.G9fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAGATGACCCAGGAAGGCCT 0.525 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false MUC16 __UNKNOWN__ hg19 19 9091790 9091791 + In_Frame_Ins INS - - ATG __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr19:9091790_9091791insATG ENST00000397910.4 - 1 229 c.24_25insCAT c.(22-27)cctggg>cctCATggg p.8_9insH __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAGATGACCCAGGAAGGCCT 0.525 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf index b33efd61a23..824a83ad379 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##Funcotator Version=0.0.5 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 -##GATKCommandLine= +##GATKCommandLine= ##INFO= ##contig= ##contig= @@ -188,11 +188,11 @@ chr1 6556585 exm9669 G A . PASS FUNCOTATION=[PLEKHG5|hg19|chr1|6556585|6556585|M chr1 6635345 indel.549 TC T . PASS FUNCOTATION=[TAS1R1|hg19|chr1|6635346|6635346|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:6635346delC|ENST00000333172.6|+|3|1346|c.1154delC|c.(1153-1155)tctfs|p.S385fs|0.600997506234414|TCCATGAGTTCTGCCTACAAC|TAS1R1_ENST00000351136.3_INTRON/TAS1R1_ENST00000328191.4_FRAME_SHIFT_DEL_p.S385fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|TAS1R1:80835|false|true|true|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|867182312|6635346|false|false|0|false|0|false||false|false|false|DIV|false|0x050000081205000402000200|1|false|147|rs867182312] chr1 7897138 indel.606 CA C . PASS FUNCOTATION=[PER3|hg19|chr1|7897139|7897139|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr1:7897139delA|ENST00000377532.3|+|20|3702|c.3479delA|c.(3478-3480)caafs|p.K1161fs|0.3940149625935162|TCTCATGGGCAAAAGGAGGAG|PER3_ENST00000361923.2_FRAME_SHIFT_DEL_p.K1152fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PER3:8863|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|773961726|7897139|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs773961726] chr1 7913430 rs228648 G A . PASS FUNCOTATION=[UTS2|hg19|chr1|7913430|7913430|DE_NOVO_START_IN_FRAME||SNP|G|G|A|g.chr1:7913430G>A|ENST00000377516.2|-|1|||||0.3566084788029925|GCAAAGAGACGTGGATTTATG|UTS2_ENST00000054668.5_MISSENSE_p.T21M|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.5216_%2C_0.4784|false|false|1||false|true|true|UTS2:10911|true|true|false|true|true|false|false|false|false|false|false|true|false|false|false|true|true|false|true|true|228648|7913430|false|false|0|true|0|false|0.476578_%2C_0.523422|false|false|false|SNV|true|0x050128020a0517053f000101|1|false|79|rs228648] -chr1 8045014 indel.625 GGCC G . PASS FUNCOTATION=[PARK7|hg19|chr1|8045015|8045017|IN_FRAME_DEL||DEL|GCC|GCC|-|g.chr1:8045015_8045017delGCC|ENST00000493678.1|+|7|537|c.471_473delGCC|c.(469-474)gggcct>ggt|p.P158del|0.4466501240694789|CAAGCCGGGGGCCTGGGACCAGC|PARK7_ENST00000377491.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000338639.5_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377488.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377493.5_IN_FRAME_DEL_p.P138del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|764877312|8045015|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs764877312] +chr1 8045014 indel.625 GGCC G . PASS FUNCOTATION=[PARK7|hg19|chr1|8045015|8045017|IN_FRAME_DEL||DEL|GCC|GCC|-|g.chr1:8045015_8045017delGCC|ENST00000493678.1|+|7|537_539|c.471_473delGCC|c.(469-474)gggcct>ggt|p.P158del|0.4466501240694789|CAAGCCGGGGGCCTGGGACCAGC|PARK7_ENST00000377491.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000338639.5_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377488.1_IN_FRAME_DEL_p.P158del/PARK7_ENST00000377493.5_IN_FRAME_DEL_p.P138del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PARK7:11315|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|764877312|8045015|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs764877312] chr1 9994822 indel.687 CT C . PASS FUNCOTATION=[LZIC|hg19|chr1|9994823|9994823|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:9994823delT|ENST00000377223.1|-|5|582|c.333delA|c.(331-333)gcafs|p.E112fs|0.3516209476309227|ATTTTACCTCTGCTAACCTTG|LZIC_ENST00000377213.1_FRAME_SHIFT_DEL_p.E112fs/LZIC_ENST00000400903.2_FRAME_SHIFT_DEL_p.E112fs/LZIC_ENST00000541052.1_FRAME_SHIFT_DEL_p.E133fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|LZIC:84328|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|866608629|9994823|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|147|rs866608629] chr1 10478954 indel.710 TC T . PASS FUNCOTATION=[PGD|hg19|chr1|10478955|10478955|FRAME_SHIFT_DEL||DEL|C|C|-|g.chr1:10478955delC|ENST00000270776.8|+|11|1219|c.1182delC|c.(1180-1182)ttcfs|p.F395fs|0.46384039900249374|TGGACGACTTCTTTAAGTCAG|PGD_ENST00000538557.1_FRAME_SHIFT_DEL_p.F382fs/PGD_ENST00000541529.1_FRAME_SHIFT_DEL_p.F373fs/PGD_ENST00000498356.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PGD:5226|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|767877628|10478955|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs767877628] chr1 11906068 exm15531 A G . PASS FUNCOTATION=[NPPA|hg19|chr1|11906068|11906068|NONSTOP||SNP|A|A|G|g.chr1:11906068A>G|ENST00000376480.3|-|3|553|c.454T>C|c.(454-456)Tga>Cga|p.*152R|0.4937655860349127|TGTTATCTTCAGTACTGCAAA|NPPA_ENST00000376476.1_NONSTOP_p.*102R/NPPA-AS1_ENST00000446542.1_RNA/NPPA-AS1_ENST00000400892.2_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8209_%2C_0.1791|false|false|1||false|true|false|NPPA:4878_%7C_NPPA-AS1:100379251|true|true|true|true|true|false|false|false|false|false|false|false|false|false|false|true|true|false|false|true|5065|11906068|false|false|0|true|0|false|0.737688_%2C_0.262312|true|false|false|SNV|true|0x05013808020515053f000100|1|false|52|rs5065] -chr1 12069756 indel.888 CACTT C . PASS FUNCOTATION=[MFN2|hg19|chr1|12069757|12069760|FRAME_SHIFT_DEL||DEL|ACTT|ACTT|-|g.chr1:12069757_12069760delACTT|ENST00000235329.5|+|18|2499|c.2178_2181delACTT|c.(2176-2181)tcacttfs|p.L727fs|0.5693069306930693|TTCTTGACTCACTTCAGAGCAAAG|MFN2_ENST00000444836.1_FRAME_SHIFT_DEL_p.L727fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MFN2:9927|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|772270096|12069757|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs772270096] +chr1 12069756 indel.888 CACTT C . PASS FUNCOTATION=[MFN2|hg19|chr1|12069757|12069760|FRAME_SHIFT_DEL||DEL|ACTT|ACTT|-|g.chr1:12069757_12069760delACTT|ENST00000235329.5|+|18|2499_2502|c.2178_2181delACTT|c.(2176-2181)tcacttfs|p.L727fs|0.5693069306930693|TTCTTGACTCACTTCAGAGCAAAG|MFN2_ENST00000444836.1_FRAME_SHIFT_DEL_p.L727fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MFN2:9927|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|772270096|12069757|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs772270096] chr1 12776344 exm16961 A T . PASS FUNCOTATION=[AADACL3|hg19|chr1|12776344|12776344|FIVE_PRIME_UTR||SNP|A|A|T|g.chr1:12776344A>T|ENST00000359318.5|+|1|||||0.5311720698254364|TGCTGTTGACATGGGTGAGTT|AADACL3_ENST00000332530.3_START_CODON_SNP_p.M1L|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.3435_%2C_0.6565|false|false|1||false|true|true|AADACL3:126767|true|true|false|true|true|false|false|false|false|false|false|true|false|false|false|false|false|false|false|true|3000859|12776344|true|true|0|true|0|true||false|false|false|SNV|true|0x050300000b0517053f000100|1|false|101|rs3000859] chr1 13933727 exm18587 A G . PASS FUNCOTATION=[PDPN|hg19|chr1|13933727|13933727|MISSENSE||SNP|A|A|G|g.chr1:13933727A>G|ENST00000509009.1|+|2|156|c.112A>G|c.(112-114)Atg>Gtg|p.M38V|0.42144638403990026|CGGCGTTGCCATGCCAGGTGC|PDPN_ENST00000294489.6_MISSENSE_p.M119V/PDPN_ENST00000376057.4_MISSENSE_p.M119V/PDPN_ENST00000376061.4_START_CODON_SNP_p.M1V/PDPN_ENST00000513143.1_START_CODON_SNP_p.M1V/PDPN_ENST00000475043.1_START_CODON_SNP_p.M1V/PDPN_ENST00000487038.1_START_CODON_SNP_p.M1V|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.9954_%2C_0.004593|false|false|1||false|false|false|PDPN:10630|false|true|false|true|true|false|false|false|false|false|false|true|false|false|false|false|false|false|false|true|141726617|13933727|false|false|0|false|0|false|0.990487_%2C_0.00951302|false|false|false|SNV|true|0x050000000a05040436000100|1|false|134|rs141726617] chr1 15671649 exm19151 T C . PASS FUNCOTATION=[FHAD1|hg19|chr1|15671649|15671649|MISSENSE||SNP|T|T|C|g.chr1:15671649T>C|ENST00000375998.4|+|15|2135|c.2135T>C|c.(2134-2136)aTg>aCg|p.M712T|0.571072319201995|CGGAAGAGAATGCAAGAACTG|FHAD1_ENST00000358897.4_MISSENSE_p.M712T/FHAD1_ENST00000417793.1_MISSENSE_p.M712T/FHAD1_ENST00000375999.3_MISSENSE_p.M712T/FHAD1_ENST00000314740.8_START_CODON_SNP_p.M1T/FHAD1_ENST00000471347.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|FHAD1:114827_%7C_LOC101927417:101927417|false|true|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|true|true|200826682|15671649|false|false|0|false|0|false|0.999554_%2C_0.000446459|false|false|false|SNV|true|0x050000020a05040402000100|1|false|137|rs200826682] @@ -246,45 +246,45 @@ chr3 178936089 . C CGT . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936089|178936090| chr3 178936089 . C CGTC . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936089|178936090|IN_FRAME_INS||INS|-|-|GTC|g.chr3:178936089_178936090insGTC|ENST00000263967.3|+|10|1788|c.1631_1632insGTC|c.(1630-1632)act>acGTCt|p.544_545insS|0.3|CTGAAATCACTGAGCAGGAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936089 . C CGTCG . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936089|178936090|FRAME_SHIFT_INS||INS|-|-|GTCG|g.chr3:178936089_178936090insGTCG|ENST00000263967.3|+|10|1788|c.1631_1632insGTCG|c.(1630-1632)actfs|p.E545fs|0.3|CTGAAATCACTGAGCAGGAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936089 . CT C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936090|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr3:178936090delT|ENST00000263967.3|+|10|1788|c.1632delT|c.(1630-1632)actfs|p.E545fs|0.29925187032418954|CTGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTG C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_DEL||DEL|TG|TG|-|g.chr3:178936090_178936091delTG|ENST00000263967.3|+|10|1788|c.1632_1633delTG|c.(1630-1635)actgagfs|p.E545fs|0.29850746268656714|CTGAAATCACTGAGCAGGAGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTGA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936092|IN_FRAME_DEL||DEL|TGA|TGA|-|g.chr3:178936090_178936092delTGA|ENST00000263967.3|+|10|1788|c.1632_1634delTGA|c.(1630-1635)actgag>acg|p.E545del|0.2977667493796526|CTGAAATCACTGAGCAGGAGAAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTGAG C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936093|FRAME_SHIFT_DEL||DEL|TGAG|TGAG|-|g.chr3:178936090_178936093delTGAG|ENST00000263967.3|+|10|1788|c.1632_1635delTGAG|c.(1630-1635)actgagfs|p.E545fs|0.2995049504950495|CTGAAATCACTGAGCAGGAGAAAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTGAGCA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936095|IN_FRAME_DEL||DEL|TGAGCA|TGAGCA|-|g.chr3:178936090_178936095delTGAGCA|ENST00000263967.3|+|10|1788|c.1632_1637delTGAGCA|c.(1630-1638)actgagcag>acg|p.EQ545del|0.29802955665024633|CTGAAATCACTGAGCAGGAGAAAGAT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTGAGCAGGA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936098|IN_FRAME_DEL||DEL|TGAGCAGGA|TGAGCAGGA|-|g.chr3:178936090_178936098delTGAGCAGGA|ENST00000263967.3|+|10|1788|c.1632_1640delTGAGCAGGA|c.(1630-1641)actgagcaggag>acg|p.EQE545del|0.29584352078239606|CTGAAATCACTGAGCAGGAGAAAGATTTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936089 . CTGAGC CGTCCA . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936089|178936094|MISSENSE||ONP|CTGAGC|CTGAGC|CGTCCA|g.chr3:178936089_178936094CTGAGC>CGTCCA|ENST00000263967.3|+|10|1788|c.1631_1636CTGAGC>CGTCCA|c.(1630-1638)acTGAGCag>acGTCCAag|p.545_546EQ>SK|0.29802955665024633|TCTGAAATCACTGAGCAGGAGAAAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTG C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_DEL||DEL|TG|TG|-|g.chr3:178936090_178936091delTG|ENST00000263967.3|+|10|1788_1789|c.1632_1633delTG|c.(1630-1635)actgagfs|p.E545fs|0.29850746268656714|CTGAAATCACTGAGCAGGAGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTGA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936092|IN_FRAME_DEL||DEL|TGA|TGA|-|g.chr3:178936090_178936092delTGA|ENST00000263967.3|+|10|1788_1790|c.1632_1634delTGA|c.(1630-1635)actgag>acg|p.E545del|0.2977667493796526|CTGAAATCACTGAGCAGGAGAAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTGAG C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936093|FRAME_SHIFT_DEL||DEL|TGAG|TGAG|-|g.chr3:178936090_178936093delTGAG|ENST00000263967.3|+|10|1788_1791|c.1632_1635delTGAG|c.(1630-1635)actgagfs|p.E545fs|0.2995049504950495|CTGAAATCACTGAGCAGGAGAAAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTGAGCA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936095|IN_FRAME_DEL||DEL|TGAGCA|TGAGCA|-|g.chr3:178936090_178936095delTGAGCA|ENST00000263967.3|+|10|1788_1793|c.1632_1637delTGAGCA|c.(1630-1638)actgagcag>acg|p.EQ545del|0.29802955665024633|CTGAAATCACTGAGCAGGAGAAAGAT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTGAGCAGGA C . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936098|IN_FRAME_DEL||DEL|TGAGCAGGA|TGAGCAGGA|-|g.chr3:178936090_178936098delTGAGCAGGA|ENST00000263967.3|+|10|1788_1796|c.1632_1640delTGAGCAGGA|c.(1630-1641)actgagcaggag>acg|p.EQE545del|0.29584352078239606|CTGAAATCACTGAGCAGGAGAAAGATTTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936089 . CTGAGC CGTCCA . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936089|178936094|MISSENSE||ONP|CTGAGC|CTGAGC|CGTCCA|g.chr3:178936089_178936094CTGAGC>CGTCCA|ENST00000263967.3|+|10|1788_1793|c.1631_1636CTGAGC>CGTCCA|c.(1630-1638)acTGAGCag>acGTCCAag|p.545_546EQ>SK|0.29802955665024633|TCTGAAATCACTGAGCAGGAGAAAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TA . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_INS||INS|-|-|A|g.chr3:178936090_178936091insA|ENST00000263967.3|+|10|1789|c.1632_1633insA|c.(1633-1635)gagfs|p.E545fs|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TAT . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_INS||INS|-|-|AT|g.chr3:178936090_178936091insAT|ENST00000263967.3|+|10|1789|c.1632_1633insAT|c.(1633-1635)gagfs|p.E545fs|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TATT . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|IN_FRAME_INS||INS|-|-|ATT|g.chr3:178936090_178936091insATT|ENST00000263967.3|+|10|1789|c.1632_1633insATT|c.(1633-1635)gag>ATTgag|p.544_545insI|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TATTG . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_INS||INS|-|-|ATTG|g.chr3:178936090_178936091insATTG|ENST00000263967.3|+|10|1789|c.1632_1633insATTG|c.(1633-1635)gagfs|p.E545fs|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . TG T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936091|FRAME_SHIFT_DEL||DEL|G|G|-|g.chr3:178936091delG|ENST00000263967.3|+|10|1789|c.1633delG|c.(1633-1635)gagfs|p.E545fs|0.29925187032418954|TGAAATCACTGAGCAGGAGAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936090 . TGA T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936092|FRAME_SHIFT_DEL||DEL|GA|GA|-|g.chr3:178936091_178936092delGA|ENST00000263967.3|+|10|1789|c.1633_1634delGA|c.(1633-1635)gagfs|p.E545fs|0.29850746268656714|TGAAATCACTGAGCAGGAGAAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936090 . TGAG T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936093|IN_FRAME_DEL||DEL|GAG|GAG|-|g.chr3:178936091_178936093delGAG|ENST00000263967.3|+|10|1789|c.1633_1635delGAG|c.(1633-1635)gagdel|p.E545del|0.3002481389578164|TGAAATCACTGAGCAGGAGAAAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936090 . TGAGC T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936094|FRAME_SHIFT_DEL||DEL|GAGC|GAGC|-|g.chr3:178936091_178936094delGAGC|ENST00000263967.3|+|10|1789|c.1633_1636delGAGC|c.(1633-1638)gagcagfs|p.E545fs|0.2995049504950495|TGAAATCACTGAGCAGGAGAAAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr3 178936090 . TGAGCAG T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936096|IN_FRAME_DEL||DEL|GAGCAG|GAGCAG|-|g.chr3:178936091_178936096delGAGCAG|ENST00000263967.3|+|10|1789|c.1633_1638delGAGCAG|c.(1633-1638)gagcagdel|p.EQ545del|0.29802955665024633|TGAAATCACTGAGCAGGAGAAAGATT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936090 . TGA T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936092|FRAME_SHIFT_DEL||DEL|GA|GA|-|g.chr3:178936091_178936092delGA|ENST00000263967.3|+|10|1789_1790|c.1633_1634delGA|c.(1633-1635)gagfs|p.E545fs|0.29850746268656714|TGAAATCACTGAGCAGGAGAAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936090 . TGAG T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936093|IN_FRAME_DEL||DEL|GAG|GAG|-|g.chr3:178936091_178936093delGAG|ENST00000263967.3|+|10|1789_1791|c.1633_1635delGAG|c.(1633-1635)gagdel|p.E545del|0.3002481389578164|TGAAATCACTGAGCAGGAGAAAG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936090 . TGAGC T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936094|FRAME_SHIFT_DEL||DEL|GAGC|GAGC|-|g.chr3:178936091_178936094delGAGC|ENST00000263967.3|+|10|1789_1792|c.1633_1636delGAGC|c.(1633-1638)gagcagfs|p.E545fs|0.2995049504950495|TGAAATCACTGAGCAGGAGAAAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr3 178936090 . TGAGCAG T . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936091|178936096|IN_FRAME_DEL||DEL|GAGCAG|GAGCAG|-|g.chr3:178936091_178936096delGAGCAG|ENST00000263967.3|+|10|1789_1794|c.1633_1638delGAGCAG|c.(1633-1638)gagcagdel|p.EQ545del|0.29802955665024633|TGAAATCACTGAGCAGGAGAAAGATT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TGAG . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|IN_FRAME_INS||INS|-|-|GAG|g.chr3:178936090_178936091insGAG|ENST00000263967.3|+|10|1789|c.1632_1633insGAG|c.(1633-1635)gag>GAGgag|p.544_545insE|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr3 178936090 . T TGAGC . PASS FUNCOTATION=[PIK3CA|hg19|chr3|178936090|178936091|FRAME_SHIFT_INS||INS|-|-|GAGC|g.chr3:178936090_178936091insGAGC|ENST00000263967.3|+|10|1789|c.1632_1633insGAGC|c.(1633-1635)gagfs|p.Q546fs|0.3|TGAAATCACTGAGCAGGAGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr4 82126215 var_4_82126215 C A . PASS FUNCOTATION=[PRKG2|hg19|chr4|82126215|82126215|SPLICE_SITE|INTRON|SNP|C|C|A|g.chr4:82126215C>A|ENST00000395578.1|-|||c.e2+1G>T|c.e2-1||0.4513715710723192|GCTCAGGGACCTGAGAAGGCA|PRKG2_ENST00000264399.1_DE_NOVO_START_IN_FRAME/PRKG2_ENST00000418486.2_SPLICE_SITE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|true||false|false|||false|false|false|PRKG2:5593|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|866277244|82126215|false|false|0|false|0|false||false|false|false|SNV|false|0x050000200005000402000100|1|false|147|rs866277244] chr4 87028376 exm411105 G A . PASS FUNCOTATION=[MAPK10|hg19|chr4|87028376|87028376|SPLICE_SITE|SILENT|SNP|G|G|A|g.chr4:87028376G>A|ENST00000395169.3|-|5|973|c.252C>T|c.(250-252)aaC>aaT|p.N84N|0.39900249376558605|CAAAACTCACGTTTTTATGGT|MAPK10_ENST00000395166.1_SPLICE_SITE_p.N84N/MAPK10_ENST00000395160.3_DE_NOVO_START_IN_FRAME/MAPK10_ENST00000395157.3_DE_NOVO_START_IN_FRAME/MAPK10_ENST00000359221.3_SPLICE_SITE_p.N122N/MAPK10_ENST00000361569.2_SPLICE_SITE_p.N122N/MAPK10_ENST00000395161.2_SPLICE_SITE_p.N122N/MAPK10_ENST00000449047.2_DE_NOVO_START_IN_FRAME/MAPK10_ENST00000513839.1_SPLICE_SITE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|MAPK10:5602|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|true|200989776|87028376|false|true|0|false|0|true|0.999966_%2C_3.4343e-005|false|false|true|SNV|true|0x050200400305040402000100|1|false|137|rs200989776] chr5 1882759 . C CAT . PASS FUNCOTATION=[IRX4|hg19|chr5|1882759|1882760|START_CODON_INS||INS|-|-|AT|g.chr5:1882759_1882760insAT|ENST00000505790.1|-|2|460|c.2_3insAT|||0.72|CGGGTAGGACATGGCGGGCG|IRX4_ENST00000231357.2_START_CODON_INS_/IRX4_ENST00000513692.1_START_CODON_INS_|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr6 88255394 var_6_88255394 CTTT C . PASS FUNCOTATION=[RARS2|hg19|chr6|88255395|88255397|IN_FRAME_DEL||DEL|TTT|TTT|-|g.chr6:88255395_88255397delTTT|ENST00000369536.5|-|7|521|c.472_474delAAA|c.(472-474)aaadel|p.K158del|0.2903225806451613|CTAAAGCTTCTTTGAGATTTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|RARS2:57038|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|757743894|88255395|false|false|0|false|0|false|0.999966_%2C_3.4343e-005|false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs757743894] -chr10 120795681 indel.14858 TCTCGGTCTCTTG T . PASS FUNCOTATION=[EIF3A|hg19|chr10|120795682|120795693|IN_FRAME_DEL||DEL|CTCGGTCTCTTG|CTCGGTCTCTTG|-|g.chr10:120795682_120795693delCTCGGTCTCTTG|ENST00000369144.3|-|22|4147|c.4007_4018delCAAGAGACCGAG|c.(4006-4020)tcaagagaccgagaa>taa|p.1336_1340SRDRE>*|0.3859223300970874|CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG|EIF3A_ENST00000541549.1_IN_FRAME_DEL_p.1302_1306SRDRE>*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|EIF3A:8661|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|766037789|120795682|false|false|0|false|0|false||false|false|false|DIV|false|0x050000000005000402000200|1|false|144|rs766037789] -chr12 11243923 indel.23289 TTTCACC T . PASS FUNCOTATION=[TAS2R43|hg19|chr12|11243924|11243929|IN_FRAME_DEL||DEL|TTCACC|TTCACC|-|g.chr12:11243924_11243929delTTCACC|ENST00000531678.1|-|1|990|c.900_905delGGTGAA|c.(898-906)tgggtgaaa>tga|p.300_302WVK>*|0.35714285714285715|CTTCTCTCCTTTCACCCAGTACCTCA|TAS2R14_ENST00000381852.4_INTRON/PRR4_ENST00000536668.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PRH1-TAS2R14:106707243_%7C_TAS2R43:259289_%7C_PRH1:5554_%7C_PRH1-PRR4:100533464|false|true|true|false|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|867813065|11243924|false|false|0|false|0|false||false|false|false|DIV|false|0x050000080005000402000210|1|false|147|rs867813065] +chr6 88255394 var_6_88255394 CTTT C . PASS FUNCOTATION=[RARS2|hg19|chr6|88255395|88255397|IN_FRAME_DEL||DEL|TTT|TTT|-|g.chr6:88255395_88255397delTTT|ENST00000369536.5|-|7|521_523|c.472_474delAAA|c.(472-474)aaadel|p.K158del|0.2903225806451613|CTAAAGCTTCTTTGAGATTTGCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|RARS2:57038|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|757743894|88255395|false|false|0|false|0|false|0.999966_%2C_3.4343e-005|false|false|false|DIV|true|0x050000000005040402000200|1|false|144|rs757743894] +chr10 120795681 indel.14858 TCTCGGTCTCTTG T . PASS FUNCOTATION=[EIF3A|hg19|chr10|120795682|120795693|IN_FRAME_DEL||DEL|CTCGGTCTCTTG|CTCGGTCTCTTG|-|g.chr10:120795682_120795693delCTCGGTCTCTTG|ENST00000369144.3|-|22|4147_4158|c.4007_4018delCAAGAGACCGAG|c.(4006-4020)tcaagagaccgagaa>taa|p.1336_1340SRDRE>*|0.3859223300970874|CGGTCTCTTTCTCGGTCTCTTGAAAGAGCTGG|EIF3A_ENST00000541549.1_IN_FRAME_DEL_p.1302_1306SRDRE>*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|EIF3A:8661|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|766037789|120795682|false|false|0|false|0|false||false|false|false|DIV|false|0x050000000005000402000200|1|false|144|rs766037789] +chr12 11243923 indel.23289 TTTCACC T . PASS FUNCOTATION=[TAS2R43|hg19|chr12|11243924|11243929|IN_FRAME_DEL||DEL|TTCACC|TTCACC|-|g.chr12:11243924_11243929delTTCACC|ENST00000531678.1|-|1|990_995|c.900_905delGGTGAA|c.(898-906)tgggtgaaa>tga|p.300_302WVK>*|0.35714285714285715|CTTCTCTCCTTTCACCCAGTACCTCA|TAS2R14_ENST00000381852.4_INTRON/PRR4_ENST00000536668.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|PRH1-TAS2R14:106707243_%7C_TAS2R43:259289_%7C_PRH1:5554_%7C_PRH1-PRR4:100533464|false|true|true|false|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|867813065|11243924|false|false|0|false|0|false||false|false|false|DIV|false|0x050000080005000402000210|1|false|147|rs867813065] chr12 55820040 indel.25160 GA G . PASS FUNCOTATION=[OR6C76|hg19|chr12|55820041|55820041|FRAME_SHIFT_DEL||DEL|A|A|-|g.chr12:55820041delA|ENST00000328314.3|+|1|3|c.4delA|c.(4-6)aaafs|p.N3fs|0.341645885286783|ATCAGAAATGAAAAATAGAAC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|OR6C76:390326|false|true|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|768848732|55820041|false|false|0|false|0|false|0.999966_%2C_3.4343e-005|false|false|false|DIV|false|0x050000001205000402000200|1|false|144|rs768848732] chr13 60738150 . C A . PASS FUNCOTATION=[Unknown|hg19|chr13|60738150|60738150|IGR||SNP|C|C|A|g.chr13:60738150C>A|no_transcript|||||||0.6234413965087282|CCCTTCCGGGCACTGCGAAAC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr13 60738150 . CAC C . PASS FUNCOTATION=[Unknown|hg19|chr13|60738151|60738152|IGR||DEL|AC|AC|-|g.chr13:60738151_60738152delAC|no_transcript|||||||0.6218905472636815|CCTTCCGGGCACTGCGAAACAT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr13 60738150 . C CAC . PASS FUNCOTATION=[Unknown|hg19|chr13|60738150|60738151|IGR||INS|-|-|AC|g.chr13:60738150_60738151insAC|no_transcript|||||||0.6225|CCTTCCGGGCACTGCGAAAC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091787 . A ATTT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091787|9091788|IN_FRAME_INS||INS|-|-|TTT|g.chr19:9091787_9091788insTTT|ENST00000397910.4|-|1|232|c.27_28insAAA|c.(25-30)gggtca>gggAAAtca|p.9_10insK|0.5275|GAGAAGATGACCCAGGAAGG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091787 . A ATTTTTT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091787|9091788|IN_FRAME_INS||INS|-|-|TTTTTT|g.chr19:9091787_9091788insTTTTTT|ENST00000397910.4|-|1|232|c.27_28insAAAAAA|c.(25-30)gggtca>gggAAAAAAtca|p.9_10insKK|0.5275|GAGAAGATGACCCAGGAAGG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr19 9091787 . ACCCA A . PASS FUNCOTATION=[MUC16|hg19|chr19|9091788|9091791|FRAME_SHIFT_DEL||DEL|CCCA|CCCA|-|g.chr19:9091788_9091791delCCCA|ENST00000397910.4|-|1|232|c.24_27delTGGG|c.(22-27)cctgggfs|p.G9fs|0.5247524752475248|GAGAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr19 9091788 . CCCA C . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091791|IN_FRAME_DEL||DEL|CCA|CCA|-|g.chr19:9091789_9091791delCCA|ENST00000397910.4|-|1|231|c.24_26delTGG|c.(22-27)cctggg>ccg|p.G9del|0.5235732009925558|AGAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr19 9091787 . ACCCA A . PASS FUNCOTATION=[MUC16|hg19|chr19|9091788|9091791|FRAME_SHIFT_DEL||DEL|CCCA|CCCA|-|g.chr19:9091788_9091791delCCCA|ENST00000397910.4|-|1|232_235|c.24_27delTGGG|c.(22-27)cctgggfs|p.G9fs|0.5247524752475248|GAGAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr19 9091788 . CCCA C . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091791|IN_FRAME_DEL||DEL|CCA|CCA|-|g.chr19:9091789_9091791delCCA|ENST00000397910.4|-|1|231_233|c.24_26delTGG|c.(22-27)cctggg>ccg|p.G9del|0.5235732009925558|AGAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091788 . C CTAA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091788|9091789|IN_FRAME_INS||INS|-|-|TAA|g.chr19:9091788_9091789insTAA|ENST00000397910.4|-|1|231|c.26_27insTTA|c.(25-27)ggg>ggTTAg|p.9_10ins*|0.5275|AGAAGATGACCCAGGAAGGC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091788 . C CTAATAA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091788|9091789|IN_FRAME_INS||INS|-|-|TAATAA|g.chr19:9091788_9091789insTAATAA|ENST00000397910.4|-|1|231|c.26_27insTTATTA|c.(25-27)ggg>ggTTATTAg|p.9_10insY*|0.5275|AGAAGATGACCCAGGAAGGC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr19 9091789 . CCA C . PASS FUNCOTATION=[MUC16|hg19|chr19|9091790|9091791|FRAME_SHIFT_DEL||DEL|CA|CA|-|g.chr19:9091790_9091791delCA|ENST00000397910.4|-|1|230|c.24_25delTG|c.(22-24)cctfs|p.G9fs|0.5248756218905473|GAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr19 9091789 . CCA C . PASS FUNCOTATION=[MUC16|hg19|chr19|9091790|9091791|FRAME_SHIFT_DEL||DEL|CA|CA|-|g.chr19:9091790_9091791delCA|ENST00000397910.4|-|1|230_231|c.24_25delTG|c.(22-24)cctfs|p.G9fs|0.5248756218905473|GAAGATGACCCAGGAAGGCCTG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091789 . C CT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091790|FRAME_SHIFT_INS||INS|-|-|T|g.chr19:9091789_9091790insT|ENST00000397910.4|-|1|230|c.25_26insA|c.(25-27)gggfs|p.G9fs|0.5275|GAAGATGACCCAGGAAGGCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091789 . C CTA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091790|FRAME_SHIFT_INS||INS|-|-|TA|g.chr19:9091789_9091790insTA|ENST00000397910.4|-|1|230|c.25_26insTA|c.(25-27)gggfs|p.G9fs|0.5275|GAAGATGACCCAGGAAGGCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091789 . C CTAA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091790|IN_FRAME_INS||INS|-|-|TAA|g.chr19:9091789_9091790insTAA|ENST00000397910.4|-|1|230|c.25_26insTTA|c.(25-27)ggg>gTTAgg|p.G9VR|0.5275|GAAGATGACCCAGGAAGGCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091789 . C CTAATAA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091790|IN_FRAME_INS||INS|-|-|TAATAA|g.chr19:9091789_9091790insTAATAA|ENST00000397910.4|-|1|230|c.25_26insTTATTA|c.(25-27)ggg>gTTATTAgg|p.G9VIR|0.5275|GAAGATGACCCAGGAAGGCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr19 9091789 . CCAGGA CGTCCT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091794|MISSENSE||ONP|CCAGGA|CCAGGA|CGTCCT|g.chr19:9091789_9091794CCAGGA>CGTCCT|ENST00000397910.4|-|1|230|c.21_26TCCTGG>AGGACG|c.(19-27)ctTCCTGgg>ctAGGACgg|p.8_9PG>GR|0.5246305418719212|AGAAGATGACCCAGGAAGGCCTGAGG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr19 9091789 . CCAGGA CGTCCT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091789|9091794|MISSENSE||ONP|CCAGGA|CCAGGA|CGTCCT|g.chr19:9091789_9091794CCAGGA>CGTCCT|ENST00000397910.4|-|1|230_235|c.21_26TCCTGG>AGGACG|c.(19-27)ctTCCTGgg>ctAGGACgg|p.8_9PG>GR|0.5246305418719212|AGAAGATGACCCAGGAAGGCCTGAGG||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091790 . C CA . PASS FUNCOTATION=[MUC16|hg19|chr19|9091790|9091791|FRAME_SHIFT_INS||INS|-|-|A|g.chr19:9091790_9091791insA|ENST00000397910.4|-|1|229|c.24_25insT|c.(25-27)gggfs|p.G9fs|0.525|AAGATGACCCAGGAAGGCCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091790 . C CAT . PASS FUNCOTATION=[MUC16|hg19|chr19|9091790|9091791|FRAME_SHIFT_INS||INS|-|-|AT|g.chr19:9091790_9091791insAT|ENST00000397910.4|-|1|229|c.24_25insAT|c.(25-27)gggfs|p.G9fs|0.525|AAGATGACCCAGGAAGGCCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr19 9091790 . C CATG . PASS FUNCOTATION=[MUC16|hg19|chr19|9091790|9091791|IN_FRAME_INS||INS|-|-|ATG|g.chr19:9091790_9091791insATG|ENST00000397910.4|-|1|229|c.24_25insCAT|c.(22-27)cctggg>cctCATggg|p.8_9insH|0.525|AAGATGACCCAGGAAGGCCT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.maf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.maf index 69156323cb2..fea7e9b4aa1 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.maf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.maf @@ -88,9 +88,9 @@ ## contig= ## contig= ## contig= -## GATKCommandLine= ## source=Funcotator -## Funcotator 0.0.5 | Date 20184130T024124 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 +## GATKCommandLine= +## Funcotator 0.0.5 | Date 20184831T034821 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_19_secondaryVariantClassification Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_ASSEMBLY ClinVar_rs CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Simple_Uniprot_alt_uniprot_accessions dbSNP_AC dbSNP_AF dbSNP_AN dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DP dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD Unknown __UNKNOWN__ 1 10147 10148 + IGR DEL C C - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:10147delC no_transcript __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTAACCCTAACCCCTAACCCT 0.4463840399002494 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown __UNKNOWN__ 1 10391 10476 + IGR DEL CCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA CCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:10391_10433delCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA no_transcript __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCC 0.5801354401805869 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false @@ -168,14 +168,14 @@ CPSF3L __UNKNOWN__ hg19 1 1260009 1260010 + 5'UTR INS - - C 575875502 byFrequen GLTPD1 __UNKNOWN__ hg19 1 1260168 1260168 + 5'UTR SNP C C A 61766199 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1260168C>A ENST00000343938.4 + 1 GLTPD1_ENST00000464957.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGGGCGGGGCGGTGGGCGGG 0.7605985037406484 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.2911,0.7089 false false 1 false true true CPTP:80772|CPSF3L:54973|GLTPD1:80772 true false false true true false false false false false false false false false false false false false true false false false 0 true 0 false 0.328697,0.671303 false false true SNV 0x050100420005170136000100 1 false 129 rs61766199 1260168 true DVL1 __UNKNOWN__ hg19 1 1284490 1284490 + 5'UTR SNP G G A 150789461 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1284490G>A ENST00000378888.5 - 1 DVL1_ENST00000378891.5_5'UTR __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCCGGCCCGGGGCTCGGACG 0.7805486284289277 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.237,0.763 false false 1 false true true LOC101929103:101929103|DVL1:1855 false false false true true false false false false false false false false false false false false true false false false false 0 true 0 false 0.238048,0.761952 false false true SNV 0x050100440005170036000100 1 false 134 rs150789461 1284490 true MIB2 __UNKNOWN__ hg19 1 1558792 1558792 + Missense_Mutation SNP T T C 12755088 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1558792T>C ENST00000505820.2 + 3 322 c.305T>C c.(304-306)aTg>aCg p.M102T MIB2_ENST00000520777.1_Missense_Mutation_p.M102T|MIB2_ENST00000504599.1_START_CODON_SNP_p.M1T|MIB2_ENST00000355826.5_Intron|MIB2_ENST00000378708.1_Intron|MIB2_ENST00000518681.1_Missense_Mutation_p.M102T|MIB2_ENST00000378712.1_Intron|MIB2_ENST00000357210.4_Missense_Mutation_p.M45T|MIB2_ENST00000360522.4_Missense_Mutation_p.M45T|MIB2_ENST00000378710.3_Missense_Mutation_p.M45T|MIB2_ENST00000512004.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGCCCACCATGGACCCCTCT 0.7281795511221946 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.2264,0.7736,. false false 1 false true false MIB2:142678 true true true true true false false false false false false true false false false false false false false true false false 0 true 0 false false false false SNV 0x050100080a0515053e000100 1 false 121 rs12755088 1558792 true -CDK11A __UNKNOWN__ hg19 1 1640295 1640312 + In_Frame_Del DEL TCCTCCTCC TCCTCCTCC - 199942750 by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1640295_1640303delTCCTCCTCC ENST00000358779.5 - 9 992 c.903_911delGGAGGAGGA c.(901-912)gaggaggaggaa>gaa p.EEE302del CDK11A_ENST00000356200.3_In_Frame_Del_p.EEE278del|CDK11A_ENST00000378633.1_In_Frame_Del_p.EEE315del|CDK11A_ENST00000404249.3_In_Frame_Del_p.EEE312del|CDK11A_ENST00000357760.2_In_Frame_Del_p.EEE311del|CDK11A_ENST00000378638.2_In_Frame_Del_p.EEE278del|CDK11A_ENST00000378635.3_3'UTR|RP1-283E3.8_ENST00000598846.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTCTTCCTCTTCCTCCTCCTCCTCCTCTG 0.5794621026894865 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false CDK11A:728642 false false false true false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x05000000000500001e000200 1 false 137 rs199942750 1640295 false +CDK11A __UNKNOWN__ hg19 1 1640295 1640312 + In_Frame_Del DEL TCCTCCTCC TCCTCCTCC - 199942750 by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1640295_1640303delTCCTCCTCC ENST00000358779.5 - 9 992_1000 c.903_911delGGAGGAGGA c.(901-912)gaggaggaggaa>gaa p.EEE302del CDK11A_ENST00000356200.3_In_Frame_Del_p.EEE278del|CDK11A_ENST00000378633.1_In_Frame_Del_p.EEE315del|CDK11A_ENST00000404249.3_In_Frame_Del_p.EEE312del|CDK11A_ENST00000357760.2_In_Frame_Del_p.EEE311del|CDK11A_ENST00000378638.2_In_Frame_Del_p.EEE278del|CDK11A_ENST00000378635.3_3'UTR|RP1-283E3.8_ENST00000598846.1_RNA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTCTTCCTCTTCCTCCTCCTCCTCCTCTG 0.5794621026894865 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false CDK11A:728642 false false false true false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x05000000000500001e000200 1 false 137 rs199942750 1640295 false NADK __UNKNOWN__ hg19 1 1684347 1684348 + In_Frame_Ins INS - - CCT 150880809|71578334|765479702 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1684347_1684348insCCT ENST00000344463.4 - 14 1994 c.1771_1772insAGG c.(1771-1773)ggc>gAGGgc p.590_591insE NADK_ENST00000378625.1_In_Frame_Ins_p.590_591insE|NADK_ENST00000341426.5_In_Frame_Ins_p.445_446insE|NADK_ENST00000341991.3_In_Frame_Ins_p.445_446insE|NADK_ENST00000342348.5_In_Frame_Ins_p.413_414insE __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTGACCTAGCCCTCCTCCTC 0.5825 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ || || || true|true|true false|false|false || false|false|false false|false|false || || false|false|false false|false|false false|false|false NADK:65220|NADK:65220|NADK:65220 false|true|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false true|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false 0|0|0 false|true|false 0|0|0 false|false|false || false|false|false false|false|false false|false|false DIV|DIV|DIV 0x05000000000504000e000204|0x050100000005000102000200|0x050000000005000002000200 1|1|1 false|false|false 134|130|144 rs150880809|rs71578334|rs765479702 1684347|1684349|1684350 true|false|false -TMEM52 __UNKNOWN__ hg19 1 1850628 1850645 + In_Frame_Del DEL AGCGGCAGG AGCGGCAGG - 575852588 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1850628_1850636delAGCGGCAGG ENST00000310991.3 - 1 86 c.69_77delCCTGCCGCT c.(67-78)ctcctgccgctg>ctg p.LPL24del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CACCTGCGGCAGCGGCAGGAGCGGCAGGA 0.7481662591687042 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.641,0.359 false false 1 false true true TMEM52:339456 false false false false true false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005170026000200 1 false 142 rs575852588 1850628 true +TMEM52 __UNKNOWN__ hg19 1 1850628 1850645 + In_Frame_Del DEL AGCGGCAGG AGCGGCAGG - 575852588 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:1850628_1850636delAGCGGCAGG ENST00000310991.3 - 1 86_94 c.69_77delCCTGCCGCT c.(67-78)ctcctgccgctg>ctg p.LPL24del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CACCTGCGGCAGCGGCAGGAGCGGCAGGA 0.7481662591687042 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.641,0.359 false false 1 false true true TMEM52:339456 false false false false true false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005170026000200 1 false 142 rs575852588 1850628 true MORN1 __UNKNOWN__ hg19 1 2258590 2258591 + Intron INS - - ACAC 149761185|61135926 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:2258590_2258591insACAC ENST00000378531.3 - c.e13+3008T>GTGTT AL589739.1_ENST00000600779.1_Frame_Shift_Ins_p.R5fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGACACAGAAACAGAAACAC 0.4275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.2077,0.7921|0.2077,0.7921 false|false false|false 1|1 | false|false true|false true|false MORN1:79906|MORN1:79906 false|false false|false true|true false|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x05000008000517002e000200|0x050000080005000002000200 1|1 false|false 134|129 rs149761185|rs61135926 2258590|2258593 true|false MORN1 __UNKNOWN__ hg19 1 2258627 2258630 + Intron DEL AG AG - 144331124 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:2258627_2258628delAG ENST00000378531.3 - c.e13+3044CTG>G AL589739.1_ENST00000600779.1_Frame_Shift_Del_p.R17fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACAGAGACACAGAGACACAGAA 0.39800995024875624 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8407,0.1593 false false 1 false true false MORN1:79906 false false true true true false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x05000008000515003e000200 1 false 134 rs144331124 2258627 true MORN1 __UNKNOWN__ hg19 1 2258946 2258947 + Intron INS - - A 59142249|397940423 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:2258946_2258947insA ENST00000378531.3 - c.e13+3364G>TG AL589739.1_ENST00000600779.1_Frame_Shift_Ins_p.R123fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAACAAACACAGAGACACAG 0.5075 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false | false|false false|false | | false|false true|false true|false MORN1:79906|MORN1:79906 false|false false|false true|true true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false 0.755924,0.244076| false|false false|false false|false DIV|DIV 0x05000008000507001e000200|0x050000080005000002000200 1|1 false|false 138|138 rs59142249|rs397940423 2258946|2258947 true|false -ACTRT2 __UNKNOWN__ hg19 1 2938408 2938413 + In_Frame_Del DEL AGA AGA - 4013154 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:2938408_2938410delAGA ENST00000378404.2 + 1 362 c.158_160delAGA c.(157-162)cagaag>cag p.K54del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGGCCAACCAGAAGAAGTACTT 0.5905707196029777 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8876,0.1124 false false 1 false true false ACTRT2:140625 false false false true true false false false false false false false false false false false false false false false true false 0 false 0 false 0.890652,0.109348 false false false DIV 0x05000000000515003e000200 1 false 108 rs4013154 2938408 true -ESPN __UNKNOWN__ hg19 1 6509022 6509045 + In_Frame_Del DEL CCACCGCCGCCC CCACCGCCGCCC - 548962140 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:6509022_6509033delCCACCGCCGCCC ENST00000377828.1 + 8 1953 c.1786_1797delCCACCGCCGCCC c.(1786-1797)ccaccgccgcccdel p.PPPP596del ESPN_ENST00000461727.1_In_Frame_Del_p.PPPP30del|ESPN_ENST00000416731.1_In_Frame_Del_p.PPPP30del|ESPN_ENST00000475228.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAGGGAGCTGCCACCGCCGCCCCCACCGCCGC 0.7718446601941747 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.9984,0.001597 false false 0 false false false ESPN:83715 false false false false true false false false false false false false false false false false false false false false false false 0 false 0 false 0.997047,0.0029535 false false false DIV 0x050000000005040026000200 1 false 142 rs548962140 6509022 true +ACTRT2 __UNKNOWN__ hg19 1 2938408 2938413 + In_Frame_Del DEL AGA AGA - 4013154 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:2938408_2938410delAGA ENST00000378404.2 + 1 362_364 c.158_160delAGA c.(157-162)cagaag>cag p.K54del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GAGGCCAACCAGAAGAAGTACTT 0.5905707196029777 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8876,0.1124 false false 1 false true false ACTRT2:140625 false false false true true false false false false false false false false false false false false false false false true false 0 false 0 false 0.890652,0.109348 false false false DIV 0x05000000000515003e000200 1 false 108 rs4013154 2938408 true +ESPN __UNKNOWN__ hg19 1 6509022 6509045 + In_Frame_Del DEL CCACCGCCGCCC CCACCGCCGCCC - 548962140 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:6509022_6509033delCCACCGCCGCCC ENST00000377828.1 + 8 1953_1964 c.1786_1797delCCACCGCCGCCC c.(1786-1797)ccaccgccgcccdel p.PPPP596del ESPN_ENST00000461727.1_In_Frame_Del_p.PPPP30del|ESPN_ENST00000416731.1_In_Frame_Del_p.PPPP30del|ESPN_ENST00000475228.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAGGGAGCTGCCACCGCCGCCCCCACCGCCGC 0.7718446601941747 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.9984,0.001597 false false 0 false false false ESPN:83715 false false false false true false false false false false false false false false false false false false false false false false 0 false 0 false 0.997047,0.0029535 false false false DIV 0x050000000005040026000200 1 false 142 rs548962140 6509022 true UTS2 __UNKNOWN__ hg19 1 7913430 7913430 + DE_NOVO_START_IN_FRAME SNP G G A 228648 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:7913430G>A ENST00000377516.2 - 1 UTS2_ENST00000054668.5_Missense_Mutation_p.T21M __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCAAAGAGACGTGGATTTATG 0.3566084788029925 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.5216,0.4784 false false 1 false true true UTS2:10911 true true false true true false false false false false false true false false false true true false true true false false 0 true 0 false 0.476578,0.523422 false false false SNV 0x050128020a0517053f000101 1 false 79 rs228648 7913430 true PTCHD2 __UNKNOWN__ hg19 1 11593793 11593794 + Intron INS - - GCACACACGCAC 113116961 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:11593793_11593794insGCACACACGCAC ENST00000294484.6 + c.e18-645T>TGCACACACGCAC PTCHD2_ENST00000304391.6_5'UTR|PTCHD2_ENST00000389575.3_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGACACGCATGCACACACAC 0.5625 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.2478,0.3878 false false 1 false false false DISP3:57540|PTCHD2:57540 true false true false true false false false false false false false false false false false false false false false false false 0 true 0 false false false false DIV 0x05010008000514012e000200 1 false 132 rs113116961 11593793 true FBXO2 __UNKNOWN__ hg19 1 11710779 11710780 + In_Frame_Ins INS - - GCG 148874459|538764329 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:11710779_11710780insGCG ENST00000354287.4 - 2 477 c.134_135insCGC c.(133-135)gcg>gcCGCg p.45_46insA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTCCAGGTACGCGGCGGCGG 0.7275 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.6534,0.3103|0.6534,0.3103 false|false false|false 1|1 | false|false false|true false|true FBXO2:26232|FBXO2:26232 false|false false|false false|false false|false false|true false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x05000000000504000e000200|0x050000000005170024000200 1|1 false|false 134|142 rs148874459|rs538764329 11710779|11710782 true|true @@ -185,7 +185,7 @@ PRAMEF7 __UNKNOWN__ hg19 1 12980232 12980232 + Silent SNP G G A 9328937 byFrequ PRDM2 __UNKNOWN__ hg19 1 14106394 14106395 + In_Frame_Ins INS - - CTC 2308040|59028030 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:14106394_14106395insCTC ENST00000235372.7 + 8 2960 c.2104_2105insCTC c.(2104-2106)act>aCTCct p.702_703insP PRDM2_ENST00000413440.1_In_Frame_Ins_p.501_502insP|PRDM2_ENST00000343137.4_In_Frame_Ins_p.501_502insP|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_In_Frame_Ins_p.702_703insP __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GATAAACTAACTCCTGCAGG 0.4875 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false | false|false false|false | | false|false true|false true|false PRDM2:7799|PRDM2:7799 true|true false|false true|true true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|false false|false 0|0 true|true 0|0 false|false | false|false false|false false|false DIV|DIV 0x05010008000507011e000200|0x050100080005000102000200 1|1 false|false 100|138 rs2308040|rs59028030 14106394|14106399 true|false FHAD1 __UNKNOWN__ hg19 1 15714854 15714855 + Intron INS - - TCCCTCCCTCCCTCCCTCCT __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:15714854_15714855insTCCCTCCCTCCCTCCCTCCT ENST00000375998.4 + c.e29+6165C>CTCCCTCCCTCCCTCCCTCCT FHAD1_ENST00000358897.4_Intron|FHAD1_ENST00000417793.1_Intron|FHAD1_ENST00000375999.3_Nonstop_Mutation_p.A1448fs|FHAD1_ENST00000314740.8_Intron|FHAD1_ENST00000471347.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CTGCCCCACCTGCCTGCAGT 0.6025 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false CASP9 __UNKNOWN__ hg19 1 15820307 15820308 + Intron INS - - C 2234723|397776921 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:15820307_15820308insC ENST00000333868.5 - c.e8-80T>GT CASP9_ENST00000546424.1_Frame_Shift_Ins_p.V413fs|CASP9_ENST00000348549.5_Intron|CASP9_ENST00000375890.4_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCCTGCTCACCCCAAATCC 0.575 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.7642,0.2358|0.7642,0.2358 false|false false|false 1|1 | false|false true|false true|false CASP9:842|CASP9:842 true|false false|false true|true true|false true|false false|false false|false false|false false|false false|false true|true false|false false|false false|false false|false false|false false|false false|false false|false true|true true|false false|false 0|0 true|false 0|0 false|false 0.700426,0.299574| false|false false|false false|false DIV|DIV 0x05010008120517013e000201|0x050000081205000002000200 1|1 false|false 98|138 rs2234723|rs397776921 15820307|15820311 true|false -SPEN __UNKNOWN__ hg19 1 16262476 16262479 + Frame_Shift_Del DEL TG TG - 765451626 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:16262476_16262477delTG ENST00000375759.3 + 11 9944 c.9741_9742delTG c.(9739-9744)cctgccfs p.A3248fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCCCCACCCCTGCCCCCGTCCC 0.6393034825870647 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false SPEN:23013 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205040002000200 1 false 144 rs765451626 16262476 true +SPEN __UNKNOWN__ hg19 1 16262476 16262479 + Frame_Shift_Del DEL TG TG - 765451626 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:16262476_16262477delTG ENST00000375759.3 + 11 9944_9945 c.9741_9742delTG c.(9739-9744)cctgccfs p.A3248fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCCCCACCCCTGCCCCCGTCCC 0.6393034825870647 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false SPEN:23013 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205040002000200 1 false 144 rs765451626 16262476 true AL355149.2 __UNKNOWN__ hg19 1 16865771 16865772 + Frame_Shift_Del DEL T T - 71574191|67841213|57681900 by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:16865771delT ENST00000601199.1 + 1 210 c.211delT c.(211-213)tttfs p.W72fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGAGGGCACCTTTTGGACAGA 0.5635910224438903 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ || || || true|true|true false|false|false || false|false|false false|false|false || || false|false|false false|false|false false|false|false FAM231B:100133301|FAM231B:100133301|FAM231B:100133301 true|false|false false|false|false false|false|false true|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false true|true|true false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false true|true|true false|true|false false|false|false 0|0|0 true|false|false 0|0|1 false|false|false || false|false|false false|false|false false|false|false DIV|DIV|DIV 0x05010000120500011e000200|0x050000001205000002000200|0x050000001205000002000240 1|1|1 false|false|false 130|131|129 rs71574191|rs67841213|rs57681900 16865771|16865773|16865774 false|false|false UBR4 __UNKNOWN__ hg19 1 19408294 19408295 + Intron INS - - C 67232976 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:19408294_19408295insC ENST00000375254.3 - c.e103+227C>GC UBR4_ENST00000375225.3_Frame_Shift_Ins_p.P3fs|UBR4_ENST00000375224.1_Intron|UBR4_ENST00000375267.2_Intron|UBR4_ENST00000375217.2_Intron|UBR4_ENST00000375226.2_Intron|UBR4_ENST00000543981.1_Intron|UBR4_ENST00000429347.2_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCTTCCCTGGCCCCATGTCT 0.5125 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.6306,0.3694 false false 1 false true true UBR4:23352 true false true true true false false false false false false false false false false false false false false false false false 0 true 0 false 0.627653,0.372347 false false false DIV 0x05010008000517013e000200 1 false 137 rs67232976 19408294 true PLA2G2C __UNKNOWN__ hg19 1 20501582 20501582 + Nonsense_Mutation SNP G G A 12139100 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:20501582G>A ENST00000429261.2 - 2 158 c.97C>T c.(97-99)Cga>Tga p.R33* PLA2G2C_ENST00000247992.5_Nonsense_Mutation_p.R36*|PLA2G2C_ENST00000495760.2_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AAGGCACTTCGCCCCGTGATG 0.49875311720698257 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.7598,0.2402 false false 1 false true true PLA2G2C:391013 true true false true true false false false false false false false true false false false false false false true false false 0 true 0 false 0.791916,0.208084 false false false SNV 0x05010000060517053f000100 1 false 120 rs12139100 20501582 true @@ -193,30 +193,30 @@ USP48 __UNKNOWN__ hg19 1 22033386 22033387 + Frame_Shift_Del DEL A A - 53257533 LACTBL1 __UNKNOWN__ hg19 1 23280024 23280025 + In_Frame_Ins INS - - CAC 764403246 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:23280024_23280025insCAC ENST00000426928.2 - 6 1153 c.1152_1153insGTG c.(1150-1155)gtgctg>gtgGTGctg p.384_385insV __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCAGCAGCAGCACCAGGCCC 0.765 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false LACTBL1:646262 false false false false false false false false false false false false false false false false false false false false false false 0 false 0 false false false false DIV 0x050000000005000002000200 1 false 144 rs764403246 23280024 false HNRNPR __UNKNOWN__ hg19 1 23670803 23670803 + DE_NOVO_START_IN_FRAME SNP G G C 12409193 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:23670803G>C ENST00000374616.3 - 1 HNRNPR_ENST00000374612.1_DE_NOVO_START_IN_FRAME|HNRNPR_ENST00000478691.1_DE_NOVO_START_OUT_FRAME __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TCCCCCCCCTGATGGACTGAG 0.683291770573566 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.6534,0.3466 false false 1 false true true HNRNPR:10236 true true false true true false false false false false false false false false false false false false true false false false 0 true 0 false 0.645099,0.354901 false false true SNV 0x05010042000517053e000100 1 false 120 rs12409193 23670803 true MDS2 __UNKNOWN__ hg19 1 23966894 23966895 + In_Frame_Ins INS - - AAG 3072132|5773050 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:23966894_23966895insAAG ENST00000374555.3 + 7 865 c.278_279insAAG c.(277-279)gta>gtAAGa p.93_94insR MDS2_ENST00000477916.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTGGCTTTGTAAGAAGAAAA 0.4525 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.7232,0.2768|0.7232,0.2768 false|false false|false 1|1 | false|false true|false true|false MDS2:259283|MDS2:259283 false|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|false false|false 0|0 true|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x05010000000517003e000200|0x050000000005000002000200 1|1 false|false 102|138 rs3072132|rs5773050 23966894|23966902 true|false -UBXN11 __UNKNOWN__ hg19 1 26608826 26608839 + Frame_Shift_Del DEL GGGGCCG GGGGCCG - 752317296 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608826_26608832delGGGGCCG ENST00000374222.1 - 16 1993 c.1521_1527delCGGCCCC c.(1519-1527)cccggccccfs p.G508fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G508fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G388fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G475fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G265fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G475fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GACAGGGACTGGGGCCGGGACCGGGAC 0.7002457002457002 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs752317296 26608826 false -UBXN11 __UNKNOWN__ hg19 1 26608836 26608869 + Frame_Shift_Del DEL CCGGGACCGGGACTGGG CCGGGACCGGGACTGGG - 757094832 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608836_26608852delCCGGGACCGGGACTGGG ENST00000374222.1 - 16 1983 c.1501_1517delCCCAGTCCCGGTCCCGG c.(1501-1518)cccagtcccggtcccggtfs p.P501fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.P501fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.P381fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.P468fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.P258fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.P468fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCG 0.6954436450839329 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs757094832 26608836 false -UBXN11 __UNKNOWN__ hg19 1 26608866 26608869 + Frame_Shift_Del DEL CC CC - 764852231 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608866_26608867delCC ENST00000374222.1 - 16 1953 c.1486_1487delGG c.(1486-1488)ggtfs p.G496fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G496fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G376fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G463fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G253fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G463fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGGACCGGGACCGGGACTGGGG 0.6865671641791045 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs764852231 26608866 false -UBXN11 __UNKNOWN__ hg19 1 26608869 26608924 + Frame_Shift_Del DEL GGACTGGGGCCGGGACCGGGACCGGGAC GGACTGGGGCCGGGACCGGGACCGGGAC - 757886085 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608869_26608896delGGACTGGGGCCGGGACCGGGACCGGGAC ENST00000374222.1 - 16 1950 c.1457_1484delGTCCCGGTCCCGGTCCCGGCCCCAGTCC c.(1456-1485)tgtcccggtcccggtcccggccccagtcccfs p.C486fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.C486fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.C366fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.C453fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.C243fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.C453fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACAGGGACCAGG 0.6892523364485982 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205040002000200 1 false 144 rs757886085 26608869 true -PHACTR4 __UNKNOWN__ hg19 1 28800351 28800362 + In_Frame_Del DEL CAGAAA CAGAAA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800351_28800356delCAGAAA ENST00000373836.3 + 6 1352 c.1139_1144delCAGAAA c.(1138-1146)ccagaaatt>ctt p.380_382PEI>L PHACTR4_ENST00000373839.3_In_Frame_Del_p.370_372PEI>L|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGTTGTGCCAGAAATTGAGTTTCC 0.5246305418719212 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -PHACTR4 __UNKNOWN__ hg19 1 28800359 28800364 + In_Frame_Del DEL GAG GAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800359_28800361delGAG ENST00000373836.3 + 6 1360 c.1147_1149delGAG c.(1147-1149)gagdel p.E383del PHACTR4_ENST00000373839.3_In_Frame_Del_p.E373del|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCAGAAATTGAGTTTCCACCAT 0.5260545905707196 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +UBXN11 __UNKNOWN__ hg19 1 26608826 26608839 + Frame_Shift_Del DEL GGGGCCG GGGGCCG - 752317296 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608826_26608832delGGGGCCG ENST00000374222.1 - 16 1993_1999 c.1521_1527delCGGCCCC c.(1519-1527)cccggccccfs p.G508fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G508fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G388fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G475fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G265fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G475fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GACAGGGACTGGGGCCGGGACCGGGAC 0.7002457002457002 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs752317296 26608826 false +UBXN11 __UNKNOWN__ hg19 1 26608836 26608869 + Frame_Shift_Del DEL CCGGGACCGGGACTGGG CCGGGACCGGGACTGGG - 757094832 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608836_26608852delCCGGGACCGGGACTGGG ENST00000374222.1 - 16 1983_1999 c.1501_1517delCCCAGTCCCGGTCCCGG c.(1501-1518)cccagtcccggtcccggtfs p.P501fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.P501fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.P381fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.P468fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.P258fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.P468fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCG 0.6954436450839329 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs757094832 26608836 false +UBXN11 __UNKNOWN__ hg19 1 26608866 26608869 + Frame_Shift_Del DEL CC CC - 764852231 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608866_26608867delCC ENST00000374222.1 - 16 1953_1954 c.1486_1487delGG c.(1486-1488)ggtfs p.G496fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G496fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G376fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G463fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G253fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G463fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGGACCGGGACCGGGACTGGGG 0.6865671641791045 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205000002000200 1 false 144 rs764852231 26608866 false +UBXN11 __UNKNOWN__ hg19 1 26608869 26608924 + Frame_Shift_Del DEL GGACTGGGGCCGGGACCGGGACCGGGAC GGACTGGGGCCGGGACCGGGACCGGGAC - 757886085 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:26608869_26608896delGGACTGGGGCCGGGACCGGGACCGGGAC ENST00000374222.1 - 16 1950_1977 c.1457_1484delGTCCCGGTCCCGGTCCCGGCCCCAGTCC c.(1456-1485)tgtcccggtcccggtcccggccccagtcccfs p.C486fs UBXN11_ENST00000374221.3_Frame_Shift_Del_p.C486fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.C366fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.C453fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.C243fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.C453fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACAGGGACCAGG 0.6892523364485982 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false false false false false false UBXN11:91544 false false false false false false false false false false true false false false false false false false false true false false 0 false 0 false false false false DIV 0x050000001205040002000200 1 false 144 rs757886085 26608869 true +PHACTR4 __UNKNOWN__ hg19 1 28800351 28800362 + In_Frame_Del DEL CAGAAA CAGAAA - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800351_28800356delCAGAAA ENST00000373836.3 + 6 1352_1357 c.1139_1144delCAGAAA c.(1138-1146)ccagaaatt>ctt p.380_382PEI>L PHACTR4_ENST00000373839.3_In_Frame_Del_p.370_372PEI>L|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CAAGTTGTGCCAGAAATTGAGTTTCC 0.5246305418719212 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +PHACTR4 __UNKNOWN__ hg19 1 28800359 28800364 + In_Frame_Del DEL GAG GAG - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800359_28800361delGAG ENST00000373836.3 + 6 1360_1362 c.1147_1149delGAG c.(1147-1149)gagdel p.E383del PHACTR4_ENST00000373839.3_In_Frame_Del_p.E373del|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCAGAAATTGAGTTTCCACCAT 0.5260545905707196 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PHACTR4 __UNKNOWN__ hg19 1 28800364 28800365 + Frame_Shift_Ins INS - - TAATGATACGG __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800364_28800365insTAATGATACGG ENST00000373836.3 + 6 1366 c.1152_1153insTAATGATACGG c.(1153-1155)ccafs p.P385fs PHACTR4_ENST00000373839.3_Frame_Shift_Ins_p.P375fs|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AATTGAGTTTCCACCATCCT 0.525 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PHACTR4 __UNKNOWN__ hg19 1 28800371 28800372 + Frame_Shift_Del DEL T T - __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800371delT ENST00000373836.3 + 6 1372 c.1159delT c.(1159-1161)tccfs p.S387fs PHACTR4_ENST00000373839.3_Frame_Shift_Del_p.S377fs|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTTTCCACCATCCTTAGATCT 0.5236907730673317 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false PHACTR4 __UNKNOWN__ hg19 1 28800375 28800375 + Nonsense_Mutation SNP T T G __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:28800375T>G ENST00000373836.3 + 6 1377 c.1163T>G c.(1162-1164)tTa>tGa p.L388* PHACTR4_ENST00000373839.3_Nonsense_Mutation_p.L378*|PHACTR4_ENST00000493669.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCACCATCCTTAGATCTACAC 0.5211970074812967 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false SERINC2 __UNKNOWN__ hg19 1 31882582 31882583 + 5'UTR INS - - GCCTCA 4012494|6143179 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:31882582_31882583insGCCTCA ENST00000373710.1 + 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ATAAGGGATGGCCCTGCTCT 0.5025 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.4065,0.5935|0.4065,0.5935 false|false false|false 1|1 | false|false true|false true|false SERINC2:347735|SERINC2:347735 true|true false|false false|false false|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|true false|false true|false false|false 0|0 true|true 0|0 false|false | false|false false|false true|true DIV|DIV 0x05010042000517012e000200|0x050100420005000102000200 1|1 false|false 108|130 rs4012494|rs6143179 31882582|31882585 true|false SERINC2 __UNKNOWN__ hg19 1 31905889 31905890 + In_Frame_Ins INS - - CAG 3050461|5773362 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:31905889_31905890insCAG ENST00000373709.3 + 9 1239 c.1089_1090insCAG c.(1090-1092)cag>CAGcag p.363_364insQ SERINC2_ENST00000373710.1_In_Frame_Ins_p.372_373insQ|SERINC2_ENST00000536384.1_In_Frame_Ins_p.367_368insQ|SERINC2_ENST00000536859.1_In_Frame_Ins_p.367_368insQ|SERINC2_ENST00000491976.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGACGCCACACAGCAGCAGC 0.6025 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.261,0.739|0.261,0.739 false|false false|false 1|1 | false|false true|false true|false SERINC2:347735|SERINC2:347735 false|true false|false false|false false|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|false false|false 0|0 true|true 0|0 false|false | false|false false|false false|false DIV|DIV 0x05010000000517002e000200|0x050100000005000102000200 1|1 false|false 102|126 rs3050461|rs5773362 31905889|31905904 true|false C1orf216 __UNKNOWN__ hg19 1 36184975 36184975 + DE_NOVO_START_OUT_FRAME SNP G G A 7521021 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:36184975G>A ENST00000270815.4 - 1 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTAGATCACGTTCGTTCCCC 0.5461346633416458 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.02416,0.9758 false false 1 false true false C1orf216:127703 true true false true true false false false false false false false false false false false false false true false false false 0 true 0 false 0.025929,0.974071 false false false SNV 0x05010002000515053f000100 1 false 116 rs7521021 36184975 true -MAP7D1 __UNKNOWN__ hg19 1 36643701 36643706 + In_Frame_Del DEL AGA AGA - 141305015|3045695 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:36643701_36643703delAGA ENST00000373151.2 + 9 1822 c.1607_1609delAGA c.(1606-1611)gagaag>gag p.K537del MAP7D1_ENST00000373150.4_In_Frame_Del_p.K505del|MAP7D1_ENST00000316156.4_In_Frame_Del_p.K500del|MAP7D1_ENST00000373148.4_In_Frame_Del_p.K83del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCAGTAACGAGAAGGAGTCAGC 0.6972704714640199 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.9355,0.0645|0.9355,0.0645 false|false false|false 1|1 | false|false true|false false|false MAP7D1:55700|MAP7D1:55700 false|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|true false|false 0|0 false|true 0|0 false|false 0.973178,0.0268219| false|false false|false false|false DIV|DIV 0x05000000000515003e000200|0x050100000005000002000200 1|1 false|false 134|102 rs141305015|rs3045695 36643701|36643703 true|false +MAP7D1 __UNKNOWN__ hg19 1 36643701 36643706 + In_Frame_Del DEL AGA AGA - 141305015|3045695 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:36643701_36643703delAGA ENST00000373151.2 + 9 1822_1824 c.1607_1609delAGA c.(1606-1611)gagaag>gag p.K537del MAP7D1_ENST00000373150.4_In_Frame_Del_p.K505del|MAP7D1_ENST00000316156.4_In_Frame_Del_p.K500del|MAP7D1_ENST00000373148.4_In_Frame_Del_p.K83del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCAGTAACGAGAAGGAGTCAGC 0.6972704714640199 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.9355,0.0645|0.9355,0.0645 false|false false|false 1|1 | false|false true|false false|false MAP7D1:55700|MAP7D1:55700 false|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|true false|false 0|0 false|true 0|0 false|false 0.973178,0.0268219| false|false false|false false|false DIV|DIV 0x05000000000515003e000200|0x050100000005000002000200 1|1 false|false 134|102 rs141305015|rs3045695 36643701|36643703 true|false NT5C1A __UNKNOWN__ hg19 1 40131838 40131839 + Frame_Shift_Ins INS - - C __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:40131838_40131839insC ENST00000235628.1 - 2 206 c.205_206insG c.(205-207)cagfs p.Q69fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GTGTAGATCTGCTGCTCCTC 0.565 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false NT5C1A __UNKNOWN__ hg19 1 40131850 40131851 + Frame_Shift_Ins INS - - A __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:40131850_40131851insA ENST00000235628.1 - 2 194 c.193_194insT c.(193-195)gacfs p.D65fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TGCTCCTCGTCCATGCGAAA 0.555 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false FOXO6 __UNKNOWN__ hg19 1 41847872 41847873 + Frame_Shift_Ins INS - - GCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:41847872_41847873insGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC ENST00000372591.1 + 2 1008 c.999_1000insGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC c.(1000-1002)gccfs p.Q337fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CGGGCCGCGGGCCCGCGCCC 0.8125 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -KLF17 __UNKNOWN__ hg19 1 44596380 44596385 + In_Frame_Del DEL CAA CAA - 34057178|200059598 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:44596380_44596382delCAA ENST00000372299.3 + 3 1179 c.1122_1124delCAA c.(1120-1125)gccaac>gcc p.N375del KLF17_ENST00000476802.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCCACAGGCCAACAACAACAAT 0.5012406947890818 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.7698,0.2302|0.7698,0.2302 false|false false|false 1|1 | false|false true|false true|false KLF17:128209|KLF17:128209 false|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 1|0 false|false 0.857614,0.142386| false|false false|false false|false DIV|DIV 0x05000000000517003e000240|0x050000000005000002000200 1|1 false|false 126|137 rs34057178|rs200059598 44596380|44596388 true|false +KLF17 __UNKNOWN__ hg19 1 44596380 44596385 + In_Frame_Del DEL CAA CAA - 34057178|200059598 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:44596380_44596382delCAA ENST00000372299.3 + 3 1179_1181 c.1122_1124delCAA c.(1120-1125)gccaac>gcc p.N375del KLF17_ENST00000476802.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ACCCACAGGCCAACAACAACAAT 0.5012406947890818 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.7698,0.2302|0.7698,0.2302 false|false false|false 1|1 | false|false true|false true|false KLF17:128209|KLF17:128209 false|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 1|0 false|false 0.857614,0.142386| false|false false|false false|false DIV|DIV 0x05000000000517003e000240|0x050000000005000002000200 1|1 false|false 126|137 rs34057178|rs200059598 44596380|44596388 true|false MOB3C __UNKNOWN__ hg19 1 47080679 47080679 + Nonsense_Mutation SNP G G A 6671527 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:47080679G>A ENST00000271139.8 - 1 127 c.70C>T c.(70-72)Cga>Tga p.R24* MOB3C_ENST00000371940.1_5'UTR|MOB3C_ENST00000319928.3_Intron|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000477318.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCGACTCTTCGACTTCTCACC 0.5087281795511222 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.3578,0.6422,. false false 1 false true false MOB3C:148932 true true true true true false false false false false false true true false false false false false false true false false 0 true 0 false 0.472526,0.527474,. false false false SNV 0x050100080e0515053f000101 1 false 116 rs6671527 47080679 true FOXD2 __UNKNOWN__ hg19 1 47904668 47904669 + In_Frame_Ins INS - - CCGCAC 3046924|71053113 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:47904668_47904669insCCGCAC ENST00000334793.5 + 1 2980 c.861_862insCCGCAC c.(862-864)ccg>CCGCACccg p.287_288insPH __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGCCCCGCATCCGCACCCGC 0.795 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.03554,0.9645,.|0.03554,0.9645 false|false false|false 1|1 | false|false true|false false|false FOXD2:2306|FOXD2:2306 false|true false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|true false|false 0|0 true|true 0|0 false|false | false|false false|false false|false DIV|DIV 0x05010000000515003e000200|0x050100000005000102000200 1|1 false|false 102|130 rs3046924|rs71053113 47904668|47904686 true|false AL109659.1 __UNKNOWN__ hg19 1 48569478 48569479 + Frame_Shift_Ins INS - - TGTG 373596514|879571472 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:48569478_48569479insTGTG ENST00000601108.1 + 1 173 c.173_174insTGTG c.(172-174)tctfs p.I65fs __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGTGTGTGTCTGTGTGTGTG 0.465 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.9379,0.03135,0.03075|0.9379,0.03135,0.03075 false|false false|false 1|1 | false|false false|false false|false SKINT1L:391037|SKINT1L:391037 false|false false|false true|true false|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x050000080005140026000200|0x050000080005000002000200 1|1 false|false 138|149 rs373596514|rs879571472 48569478|48569497 true|false SLC5A9 __UNKNOWN__ hg19 1 48708228 48708228 + Nonsense_Mutation SNP G G T 850763 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:48708228G>T ENST00000438567.2 + 13 1829 c.1777G>T c.(1777-1779)Gag>Tag p.E593* SLC5A9_ENST00000236495.5_Nonsense_Mutation_p.E618*|SLC5A9_ENST00000533824.1_Nonsense_Mutation_p.E614*|SLC5A9_ENST00000471020.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCAGCCGGGGAGTGCCCTGC 0.5835411471321695 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.8862,0.1138 false false 1 false true false SLC5A9:200010 true true false true true false false false false false false false true false false false false false false true true false 0 true 0 false 0.859228,0.140772 false false false SNV 0x050100000605150537000100 1 false 86 rs850763 48708228 true -DMRTA2 __UNKNOWN__ hg19 1 50884774 50884785 + In_Frame_Del DEL CGGCGG CGGCGG - 761537995|4027495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:50884774_50884779delCGGCGG ENST00000404795.3 - 3 1586 c.1187_1192delCCGCCG c.(1186-1194)gccgccggg>ggg p.AA396del DMRTA2_ENST00000418121.1_In_Frame_Del_p.AA396del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCAGGCCCCCCGGCGGCGGCGGCGGC 0.7807881773399015 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false | false|false false|false | | false|false false|false false|false DMRTA2:63950|DMRTA2:63950 false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x050000000005000002000200|0x050000000005000002000200 1|1 false|false 144|108 rs761537995|rs4027495 50884774|50884792 false|false +DMRTA2 __UNKNOWN__ hg19 1 50884774 50884785 + In_Frame_Del DEL CGGCGG CGGCGG - 761537995|4027495 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:50884774_50884779delCGGCGG ENST00000404795.3 - 3 1586_1591 c.1187_1192delCCGCCG c.(1186-1194)gccgccggg>ggg p.AA396del DMRTA2_ENST00000418121.1_In_Frame_Del_p.AA396del __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCAGGCCCCCCGGCGGCGGCGGCGGC 0.7807881773399015 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false | false|false false|false | | false|false false|false false|false DMRTA2:63950|DMRTA2:63950 false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x050000000005000002000200|0x050000000005000002000200 1|1 false|false 144|108 rs761537995|rs4027495 50884774|50884792 false|false DMRTA2 __UNKNOWN__ hg19 1 50884775 50884776 + In_Frame_Ins INS - - GCA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:50884775_50884776insGCA ENST00000404795.3 - 3 1584 c.1190_1191insTGC c.(1189-1191)gcc>gcTGCc p.397_398insA DMRTA2_ENST00000418121.1_In_Frame_Ins_p.397_398insA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ AGGCCCCCCGGCGGCGGCGG 0.78 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -NRD1 __UNKNOWN__ hg19 1 52306064 52306069 + In_Frame_Del DEL TCT TCT - 35723519|60220085 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:52306064_52306066delTCT ENST00000354831.7 - 2 655 c.462_464delAGA c.(460-465)gaagat>gat p.E154del NRD1_ENST00000352171.7_In_Frame_Del_p.E154del|NRD1_ENST00000539524.1_In_Frame_Del_p.E22del|NRD1_ENST00000544028.1_In_Frame_Del_p.E22del|NRD1_ENST00000485608.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCATCATCATCTTCTTCTTCTT 0.36476426799007444 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.4383,0.5617|0.4383,0.5617 false|false false|false 1|1 | false|false true|false true|false NRD1:4898|NRDC:4898|NRD1:4898|NRDC:4898 false|true false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|true 0|0 false|false | false|false false|false false|false DIV|DIV 0x05000000000517003e000200|0x050100000005000102000200 1|1 false|false 126|129 rs35723519|rs60220085 52306064|52306075 true|false +NRD1 __UNKNOWN__ hg19 1 52306064 52306069 + In_Frame_Del DEL TCT TCT - 35723519|60220085 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:52306064_52306066delTCT ENST00000354831.7 - 2 655_657 c.462_464delAGA c.(460-465)gaagat>gat p.E154del NRD1_ENST00000352171.7_In_Frame_Del_p.E154del|NRD1_ENST00000539524.1_In_Frame_Del_p.E22del|NRD1_ENST00000544028.1_In_Frame_Del_p.E22del|NRD1_ENST00000485608.1_Intron __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TTCATCATCATCTTCTTCTTCTT 0.36476426799007444 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.4383,0.5617|0.4383,0.5617 false|false false|false 1|1 | false|false true|false true|false NRD1:4898|NRDC:4898|NRD1:4898|NRDC:4898 false|true false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|true 0|0 false|false | false|false false|false false|false DIV|DIV 0x05000000000517003e000200|0x050100000005000102000200 1|1 false|false 126|129 rs35723519|rs60220085 52306064|52306075 true|false DMRTB1 __UNKNOWN__ hg19 1 53925373 53925374 + In_Frame_Ins INS - - CCGCCC 575081928|766482978 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:53925373_53925374insCCGCCC ENST00000371445.3 + 1 302 c.247_248insCCGCCC c.(247-249)gcc>gCCGCCCcc p.83_84insAP __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCTGCGGCCGCCGCCCCCGC 0.7475 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ | | | true|true false|false 0.8926,0.1074|0.8926,0.1074 false|false false|false 1|1 | false|false true|false false|false DMRTB1:63948|DMRTB1:63948 false|false false|false false|false false|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false 0|0 false|false 0|0 false|false | false|false false|false false|false DIV|DIV 0x050000000005150026000200|0x050000000005000002000200 1|1 false|false 142|144 rs575081928|rs766482978 53925373|53925379 true|false TTC4 __UNKNOWN__ hg19 1 55182300 55182300 + Missense_Mutation SNP T T A 1147990 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:55182300T>A ENST00000371281.3 + 2 226 c.139T>A c.(139-141)Tcg>Acg p.S47T TTC4_ENST00000371284.5_Intron|MROH7-TTC4_ENST00000414150.2_Nonsense_Mutation_p.C1282* __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCTATTTATGTCGAGAGCGCC 0.3915211970074813 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ true false 0.3317,0.6683 false false 1 false true false TTC4:7268|MROH7-TTC4:100527960 true true false true true false false false false false false true false false false true true false false true true false 0 true 0 false 0.448314,0.551686 false false false SNV 0x050128000a0515053f000101 1 false 87 rs1147990 55182300 true PCSK9 __UNKNOWN__ hg19 1 55505552 55505553 + In_Frame_Ins INS - - CTG 45454392|113330492|35574083 byFrequency __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr1:55505552_55505553insCTG ENST00000302118.5 + 1 332 c.42_43insCTG c.(43-45)ctg>CTGctg p.14_15insL PCSK9_ENST00000452118.2_In_Frame_Ins_p.14_15insL __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GCCGCTGCCACTGCTGCTGC 0.7075 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ || || || true|true|true false|false|false || false|false|false false|false|false || || false|false|false true|false|false true|false|false PCSK9:255738|PCSK9:255738|PCSK9:255738 true|true|true false|false|false false|false|false false|false|false false|false|false false|false|true false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|false false|false|true false|false|true false|false|false true|true|true false|false|false false|false|false false|false|false 0|0|1 false|true|true 0|0|0 false|false|false || false|false|false false|false|false false|false|false DIV|DIV|DIV 0x050000020005070102000200|0x050100020005000102000200|0x050168020005040102100200 1|1|1 false|false|false 127|132|126 rs45454392|rs113330492|rs35574083 55505554|55505563|55505575 true|false|true diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf index b8ca47cb7a5..a3928efb564 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##Funcotator Version=0.0.5 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 -##GATKCommandLine= +##GATKCommandLine= ##INFO= ##contig= ##contig= @@ -167,14 +167,14 @@ chr1 1260009 . A AC 290.29 PASS FUNCOTATION=[CPSF3L|hg19|chr1|1260009|1260010|FI chr1 1260168 rs61766199 C A 1816.69 PASS FUNCOTATION=[GLTPD1|hg19|chr1|1260168|1260168|FIVE_PRIME_UTR||SNP|C|C|A|g.chr1:1260168C>A|ENST00000343938.4|+|1|||||0.7605985037406484|GAGGGCGGGGCGGTGGGCGGG|GLTPD1_ENST00000464957.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.2911_%2C_0.7089|false|false|1||false|true|true|CPTP:80772_%7C_CPSF3L:54973_%7C_GLTPD1:80772|true|false|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|true|false|61766199|1260168|false|false|0|true|0|false|0.328697_%2C_0.671303|false|false|true|SNV|true|0x050100420005170136000100|1|false|129|rs61766199] chr1 1284490 rs150789461 G A 3031.69 PASS FUNCOTATION=[DVL1|hg19|chr1|1284490|1284490|FIVE_PRIME_UTR||SNP|G|G|A|g.chr1:1284490G>A|ENST00000378888.5|-|1|||||0.7805486284289277|GCCCGGCCCGGGGCTCGGACG|DVL1_ENST00000378891.5_FIVE_PRIME_UTR|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.237_%2C_0.763|false|false|1||false|true|true|LOC101929103:101929103_%7C_DVL1:1855|false|false|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|true|false|false|150789461|1284490|false|false|0|true|0|false|0.238048_%2C_0.761952|false|false|true|SNV|true|0x050100440005170036000100|1|false|134|rs150789461] chr1 1558792 rs12755088 T C 3564.69 PASS FUNCOTATION=[MIB2|hg19|chr1|1558792|1558792|MISSENSE||SNP|T|T|C|g.chr1:1558792T>C|ENST00000505820.2|+|3|322|c.305T>C|c.(304-306)aTg>aCg|p.M102T|0.7281795511221946|CGGCCCACCATGGACCCCTCT|MIB2_ENST00000520777.1_MISSENSE_p.M102T/MIB2_ENST00000504599.1_START_CODON_SNP_p.M1T/MIB2_ENST00000355826.5_INTRON/MIB2_ENST00000378708.1_INTRON/MIB2_ENST00000518681.1_MISSENSE_p.M102T/MIB2_ENST00000378712.1_INTRON/MIB2_ENST00000357210.4_MISSENSE_p.M45T/MIB2_ENST00000360522.4_MISSENSE_p.M45T/MIB2_ENST00000378710.3_MISSENSE_p.M45T/MIB2_ENST00000512004.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.2264_%2C_0.7736_%2C_.|false|false|1||false|true|false|MIB2:142678|true|true|true|true|true|false|false|false|false|false|false|true|false|false|false|false|false|false|false|true|12755088|1558792|false|false|0|true|0|false||false|false|false|SNV|true|0x050100080a0515053e000100|1|false|121|rs12755088] -chr1 1640294 rs199942750 TTCCTCCTCC T 679.91 PASS FUNCOTATION=[CDK11A|hg19|chr1|1640295|1640303|IN_FRAME_DEL||DEL|TCCTCCTCC|TCCTCCTCC|-|g.chr1:1640295_1640303delTCCTCCTCC|ENST00000358779.5|-|9|992|c.903_911delGGAGGAGGA|c.(901-912)gaggaggaggaa>gaa|p.EEE302del|0.5794621026894865|CTCTTCCTCTTCCTCCTCCTCCTCCTCTG|CDK11A_ENST00000356200.3_IN_FRAME_DEL_p.EEE278del/CDK11A_ENST00000378633.1_IN_FRAME_DEL_p.EEE315del/CDK11A_ENST00000404249.3_IN_FRAME_DEL_p.EEE312del/CDK11A_ENST00000357760.2_IN_FRAME_DEL_p.EEE311del/CDK11A_ENST00000378638.2_IN_FRAME_DEL_p.EEE278del/CDK11A_ENST00000378635.3_THREE_PRIME_UTR/RP1-283E3.8_ENST00000598846.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|CDK11A:728642|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|199942750|1640295|false|false|0|false|0|false||false|false|false|DIV|false|0x05000000000500001e000200|1|false|137|rs199942750] +chr1 1640294 rs199942750 TTCCTCCTCC T 679.91 PASS FUNCOTATION=[CDK11A|hg19|chr1|1640295|1640303|IN_FRAME_DEL||DEL|TCCTCCTCC|TCCTCCTCC|-|g.chr1:1640295_1640303delTCCTCCTCC|ENST00000358779.5|-|9|992_1000|c.903_911delGGAGGAGGA|c.(901-912)gaggaggaggaa>gaa|p.EEE302del|0.5794621026894865|CTCTTCCTCTTCCTCCTCCTCCTCCTCTG|CDK11A_ENST00000356200.3_IN_FRAME_DEL_p.EEE278del/CDK11A_ENST00000378633.1_IN_FRAME_DEL_p.EEE315del/CDK11A_ENST00000404249.3_IN_FRAME_DEL_p.EEE312del/CDK11A_ENST00000357760.2_IN_FRAME_DEL_p.EEE311del/CDK11A_ENST00000378638.2_IN_FRAME_DEL_p.EEE278del/CDK11A_ENST00000378635.3_THREE_PRIME_UTR/RP1-283E3.8_ENST00000598846.1_RNA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|CDK11A:728642|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|199942750|1640295|false|false|0|false|0|false||false|false|false|DIV|false|0x05000000000500001e000200|1|false|137|rs199942750] chr1 1684347 rs150880809 C CCCT 1136.16 PASS FUNCOTATION=[NADK|hg19|chr1|1684347|1684348|IN_FRAME_INS||INS|-|-|CCT|g.chr1:1684347_1684348insCCT|ENST00000344463.4|-|14|1994|c.1771_1772insAGG|c.(1771-1773)ggc>gAGGgc|p.590_591insE|0.5825|TTGACCTAGCCCTCCTCCTC|NADK_ENST00000378625.1_IN_FRAME_INS_p.590_591insE/NADK_ENST00000341426.5_IN_FRAME_INS_p.445_446insE/NADK_ENST00000341991.3_IN_FRAME_INS_p.445_446insE/NADK_ENST00000342348.5_IN_FRAME_INS_p.413_414insE||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false_%7C_false|false_%7C_false_%7C_false|0_%7C_0_%7C_0|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|134_%7C_130_%7C_144|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|1_%7C_1_%7C_1|false_%7C_false_%7C_false|_%7C__%7C_|NADK:65220_%7C_NADK:65220_%7C_NADK:65220|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_true_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|150880809_%7C_71578334_%7C_765479702|false_%7C_false_%7C_false|false_%7C_false_%7C_false|0x05000000000504000e000204_%7C_0x050100000005000102000200_%7C_0x050000000005000002000200|false_%7C_false_%7C_false|true_%7C_false_%7C_false|1684347_%7C_1684349_%7C_1684350|0_%7C_0_%7C_0|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_true_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|true_%7C_false_%7C_false|rs150880809_%7C_rs71578334_%7C_rs765479702|true_%7C_true_%7C_true|false_%7C_false_%7C_false|_%7C__%7C_|DIV_%7C_DIV_%7C_DIV|false_%7C_false_%7C_false] -chr1 1850627 . CAGCGGCAGG C 711.12 PASS FUNCOTATION=[TMEM52|hg19|chr1|1850628|1850636|IN_FRAME_DEL||DEL|AGCGGCAGG|AGCGGCAGG|-|g.chr1:1850628_1850636delAGCGGCAGG|ENST00000310991.3|-|1|86|c.69_77delCCTGCCGCT|c.(67-78)ctcctgccgctg>ctg|p.LPL24del|0.7481662591687042|CACCTGCGGCAGCGGCAGGAGCGGCAGGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.641_%2C_0.359|false|false|1||false|true|true|TMEM52:339456|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|575852588|1850628|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005170026000200|1|false|142|rs575852588] +chr1 1850627 . CAGCGGCAGG C 711.12 PASS FUNCOTATION=[TMEM52|hg19|chr1|1850628|1850636|IN_FRAME_DEL||DEL|AGCGGCAGG|AGCGGCAGG|-|g.chr1:1850628_1850636delAGCGGCAGG|ENST00000310991.3|-|1|86_94|c.69_77delCCTGCCGCT|c.(67-78)ctcctgccgctg>ctg|p.LPL24del|0.7481662591687042|CACCTGCGGCAGCGGCAGGAGCGGCAGGA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.641_%2C_0.359|false|false|1||false|true|true|TMEM52:339456|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|575852588|1850628|false|false|0|false|0|false||false|false|false|DIV|true|0x050000000005170026000200|1|false|142|rs575852588] chr1 2258590 rs149761185 A AACAC 660.88 PASS FUNCOTATION=[MORN1|hg19|chr1|2258590|2258591|INTRON||INS|-|-|ACAC|g.chr1:2258590_2258591insACAC|ENST00000378531.3|-|||c.e13+3008T>GTGTT|||0.4275|AGACACAGAAACAGAAACAC|AL589739.1_ENST00000600779.1_FRAME_SHIFT_INS_p.R5fs||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|134_%7C_129|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|MORN1:79906_%7C_MORN1:79906|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.2077_%2C_0.7921_%7C_0.2077_%2C_0.7921|149761185_%7C_61135926|false_%7C_false|false_%7C_false|0x05000008000517002e000200_%7C_0x050000080005000002000200|true_%7C_false|false_%7C_false|2258590_%7C_2258593|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|true_%7C_true|_%7C_|true_%7C_false|rs149761185_%7C_rs61135926|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 2258626 rs144331124 CAG C 138.25 PASS FUNCOTATION=[MORN1|hg19|chr1|2258627|2258628|INTRON||DEL|AG|AG|-|g.chr1:2258627_2258628delAG|ENST00000378531.3|-|||c.e13+3044CTG>G|||0.39800995024875624|ACAGAGACACAGAGACACAGAA|AL589739.1_ENST00000600779.1_FRAME_SHIFT_DEL_p.R17fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8407_%2C_0.1593|false|false|1||false|true|false|MORN1:79906|false|false|true|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|144331124|2258627|false|false|0|false|0|false||false|false|false|DIV|true|0x05000008000515003e000200|1|false|134|rs144331124] chr1 2258946 rs59142249 C CA 326.29 PASS FUNCOTATION=[MORN1|hg19|chr1|2258946|2258947|INTRON||INS|-|-|A|g.chr1:2258946_2258947insA|ENST00000378531.3|-|||c.e13+3364G>TG|||0.5075|AAACAAACACAGAGACACAG|AL589739.1_ENST00000600779.1_FRAME_SHIFT_INS_p.R123fs||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|false_%7C_false|138_%7C_138|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|MORN1:79906_%7C_MORN1:79906|_%7C_|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|0.755924_%2C_0.244076_%7C_|false_%7C_false|false_%7C_false|_%7C_|59142249_%7C_397940423|false_%7C_false|false_%7C_false|0x05000008000507001e000200_%7C_0x050000080005000002000200|true_%7C_false|false_%7C_false|2258946_%7C_2258947|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|true_%7C_true|_%7C_|true_%7C_false|rs59142249_%7C_rs397940423|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] -chr1 2938407 rs4013154 CAGA C 648.25 PASS FUNCOTATION=[ACTRT2|hg19|chr1|2938408|2938410|IN_FRAME_DEL||DEL|AGA|AGA|-|g.chr1:2938408_2938410delAGA|ENST00000378404.2|+|1|362|c.158_160delAGA|c.(157-162)cagaag>cag|p.K54del|0.5905707196029777|GAGGCCAACCAGAAGAAGTACTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8876_%2C_0.1124|false|false|1||false|true|false|ACTRT2:140625|false|false|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|4013154|2938408|true|false|0|false|0|false|0.890652_%2C_0.109348|false|false|false|DIV|true|0x05000000000515003e000200|1|false|108|rs4013154] -chr1 6509021 . GCCACCGCCGCCC G 897.25 PASS FUNCOTATION=[ESPN|hg19|chr1|6509022|6509033|IN_FRAME_DEL||DEL|CCACCGCCGCCC|CCACCGCCGCCC|-|g.chr1:6509022_6509033delCCACCGCCGCCC|ENST00000377828.1|+|8|1953|c.1786_1797delCCACCGCCGCCC|c.(1786-1797)ccaccgccgcccdel|p.PPPP596del|0.7718446601941747|CAGGGAGCTGCCACCGCCGCCCCCACCGCCGC|ESPN_ENST00000461727.1_IN_FRAME_DEL_p.PPPP30del/ESPN_ENST00000416731.1_IN_FRAME_DEL_p.PPPP30del/ESPN_ENST00000475228.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.9984_%2C_0.001597|false|false|0||false|false|false|ESPN:83715|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|548962140|6509022|false|false|0|false|0|false|0.997047_%2C_0.0029535|false|false|false|DIV|true|0x050000000005040026000200|1|false|142|rs548962140] +chr1 2938407 rs4013154 CAGA C 648.25 PASS FUNCOTATION=[ACTRT2|hg19|chr1|2938408|2938410|IN_FRAME_DEL||DEL|AGA|AGA|-|g.chr1:2938408_2938410delAGA|ENST00000378404.2|+|1|362_364|c.158_160delAGA|c.(157-162)cagaag>cag|p.K54del|0.5905707196029777|GAGGCCAACCAGAAGAAGTACTT||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8876_%2C_0.1124|false|false|1||false|true|false|ACTRT2:140625|false|false|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|4013154|2938408|true|false|0|false|0|false|0.890652_%2C_0.109348|false|false|false|DIV|true|0x05000000000515003e000200|1|false|108|rs4013154] +chr1 6509021 . GCCACCGCCGCCC G 897.25 PASS FUNCOTATION=[ESPN|hg19|chr1|6509022|6509033|IN_FRAME_DEL||DEL|CCACCGCCGCCC|CCACCGCCGCCC|-|g.chr1:6509022_6509033delCCACCGCCGCCC|ENST00000377828.1|+|8|1953_1964|c.1786_1797delCCACCGCCGCCC|c.(1786-1797)ccaccgccgcccdel|p.PPPP596del|0.7718446601941747|CAGGGAGCTGCCACCGCCGCCCCCACCGCCGC|ESPN_ENST00000461727.1_IN_FRAME_DEL_p.PPPP30del/ESPN_ENST00000416731.1_IN_FRAME_DEL_p.PPPP30del/ESPN_ENST00000475228.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.9984_%2C_0.001597|false|false|0||false|false|false|ESPN:83715|false|false|false|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|548962140|6509022|false|false|0|false|0|false|0.997047_%2C_0.0029535|false|false|false|DIV|true|0x050000000005040026000200|1|false|142|rs548962140] chr1 7913430 rs228648 G A 1998.91 PASS FUNCOTATION=[UTS2|hg19|chr1|7913430|7913430|DE_NOVO_START_IN_FRAME||SNP|G|G|A|g.chr1:7913430G>A|ENST00000377516.2|-|1|||||0.3566084788029925|GCAAAGAGACGTGGATTTATG|UTS2_ENST00000054668.5_MISSENSE_p.T21M|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.5216_%2C_0.4784|false|false|1||false|true|true|UTS2:10911|true|true|false|true|true|false|false|false|false|false|false|true|false|false|false|true|true|false|true|true|228648|7913430|false|false|0|true|0|false|0.476578_%2C_0.523422|false|false|false|SNV|true|0x050128020a0517053f000101|1|false|79|rs228648] chr1 11593793 rs113116961 T TGCACACACGCAC 4110.93 PASS FUNCOTATION=[PTCHD2|hg19|chr1|11593793|11593794|INTRON||INS|-|-|GCACACACGCAC|g.chr1:11593793_11593794insGCACACACGCAC|ENST00000294484.6|+|||c.e18-645T>TGCACACACGCAC|||0.5625|AGACACGCATGCACACACAC|PTCHD2_ENST00000304391.6_FIVE_PRIME_UTR/PTCHD2_ENST00000389575.3_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.2478_%2C_0.3878|false|false|1||false|false|false|DISP3:57540_%7C_PTCHD2:57540|true|false|true|false|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|113116961|11593793|false|false|0|true|0|false||false|false|false|DIV|true|0x05010008000514012e000200|1|false|132|rs113116961] chr1 11710779 rs148874459 C CGCG 492.29 PASS FUNCOTATION=[FBXO2|hg19|chr1|11710779|11710780|IN_FRAME_INS||INS|-|-|GCG|g.chr1:11710779_11710780insGCG|ENST00000354287.4|-|2|477|c.134_135insCGC|c.(133-135)gcg>gcCGCg|p.45_46insA|0.7275|GTCCAGGTACGCGGCGGCGG|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_true|134_%7C_142|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|FBXO2:26232_%7C_FBXO2:26232|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.6534_%2C_0.3103_%7C_0.6534_%2C_0.3103|148874459_%7C_538764329|false_%7C_false|false_%7C_false|0x05000000000504000e000200_%7C_0x050000000005170024000200|false_%7C_true|false_%7C_false|11710779_%7C_11710782|0_%7C_0|false_%7C_false|false_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_true|rs148874459_%7C_rs538764329|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] @@ -184,7 +184,7 @@ chr1 12980232 rs201674075 G A 447.12 PASS FUNCOTATION=[PRAMEF7|hg19|chr1|1298023 chr1 14106394 rs2308040 A ACTC 1278.16 PASS FUNCOTATION=[PRDM2|hg19|chr1|14106394|14106395|IN_FRAME_INS||INS|-|-|CTC|g.chr1:14106394_14106395insCTC|ENST00000235372.7|+|8|2960|c.2104_2105insCTC|c.(2104-2106)act>aCTCct|p.702_703insP|0.4875|GATAAACTAACTCCTGCAGG|PRDM2_ENST00000413440.1_IN_FRAME_INS_p.501_502insP/PRDM2_ENST00000343137.4_IN_FRAME_INS_p.501_502insP/PRDM2_ENST00000376048.5_INTRON/PRDM2_ENST00000503842.1_INTRON/PRDM2_ENST00000505823.1_INTRON/PRDM2_ENST00000311066.5_IN_FRAME_INS_p.702_703insP||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|false_%7C_false|100_%7C_138|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|PRDM2:7799_%7C_PRDM2:7799|_%7C_|false_%7C_false|_%7C_|false_%7C_false|true_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|2308040_%7C_59028030|false_%7C_false|true_%7C_false|0x05010008000507011e000200_%7C_0x050100080005000102000200|true_%7C_false|false_%7C_false|14106394_%7C_14106399|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|true_%7C_true|_%7C_|false_%7C_false|true_%7C_true|_%7C_|true_%7C_false|rs2308040_%7C_rs59028030|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 15714854 . C CTCCCTCCCTCCCTCCCTCCT 171.30 PASS FUNCOTATION=[FHAD1|hg19|chr1|15714854|15714855|INTRON||INS|-|-|TCCCTCCCTCCCTCCCTCCT|g.chr1:15714854_15714855insTCCCTCCCTCCCTCCCTCCT|ENST00000375998.4|+|||c.e29+6165C>CTCCCTCCCTCCCTCCCTCCT|||0.6025|CTGCCCCACCTGCCTGCAGT|FHAD1_ENST00000358897.4_INTRON/FHAD1_ENST00000417793.1_INTRON/FHAD1_ENST00000375999.3_NONSTOP_p.A1448fs/FHAD1_ENST00000314740.8_INTRON/FHAD1_ENST00000471347.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 15820307 rs2234723 A AC 439.29 PASS FUNCOTATION=[CASP9|hg19|chr1|15820307|15820308|INTRON||INS|-|-|C|g.chr1:15820307_15820308insC|ENST00000333868.5|-|||c.e8-80T>GT|||0.575|GCCCTGCTCACCCCAAATCC|CASP9_ENST00000546424.1_FRAME_SHIFT_INS_p.V413fs/CASP9_ENST00000348549.5_INTRON/CASP9_ENST00000375890.4_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|true_%7C_true|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|98_%7C_138|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|CASP9:842_%7C_CASP9:842|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|true_%7C_false|false_%7C_false|true_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|0.700426_%2C_0.299574_%7C_|false_%7C_false|false_%7C_false|0.7642_%2C_0.2358_%7C_0.7642_%2C_0.2358|2234723_%7C_397776921|false_%7C_false|true_%7C_false|0x05010008120517013e000201_%7C_0x050000081205000002000200|true_%7C_false|false_%7C_false|15820307_%7C_15820311|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|_%7C_|false_%7C_false|true_%7C_true|_%7C_|true_%7C_false|rs2234723_%7C_rs397776921|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] -chr1 16262475 . CTG C 13.26 PASS FUNCOTATION=[SPEN|hg19|chr1|16262476|16262477|FRAME_SHIFT_DEL||DEL|TG|TG|-|g.chr1:16262476_16262477delTG|ENST00000375759.3|+|11|9944|c.9741_9742delTG|c.(9739-9744)cctgccfs|p.A3248fs|0.6393034825870647|CCCCCACCCCTGCCCCCGTCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|SPEN:23013|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|765451626|16262476|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040002000200|1|false|144|rs765451626] +chr1 16262475 . CTG C 13.26 PASS FUNCOTATION=[SPEN|hg19|chr1|16262476|16262477|FRAME_SHIFT_DEL||DEL|TG|TG|-|g.chr1:16262476_16262477delTG|ENST00000375759.3|+|11|9944_9945|c.9741_9742delTG|c.(9739-9744)cctgccfs|p.A3248fs|0.6393034825870647|CCCCCACCCCTGCCCCCGTCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|SPEN:23013|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|765451626|16262476|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040002000200|1|false|144|rs765451626] chr1 16865770 rs200788146 CT C 439.48 PASS FUNCOTATION=[AL355149.2|hg19|chr1|16865771|16865771|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:16865771delT|ENST00000601199.1|+|1|210|c.211delT|c.(211-213)tttfs|p.W72fs|0.5635910224438903|GGAGGGCACCTTTTGGACAGA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false_%7C_false|true_%7C_true_%7C_true|0_%7C_0_%7C_1|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|true_%7C_false_%7C_false|false_%7C_false_%7C_false|130_%7C_131_%7C_129|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|1_%7C_1_%7C_1|false_%7C_false_%7C_false|_%7C__%7C_|FAM231B:100133301_%7C_FAM231B:100133301_%7C_FAM231B:100133301|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|true_%7C_false_%7C_false|false_%7C_false_%7C_false|true_%7C_true_%7C_true|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|71574191_%7C_67841213_%7C_57681900|false_%7C_false_%7C_false|false_%7C_true_%7C_false|0x05010000120500011e000200_%7C_0x050000001205000002000200_%7C_0x050000001205000002000240|false_%7C_false_%7C_false|false_%7C_false_%7C_false|16865771_%7C_16865773_%7C_16865774|0_%7C_0_%7C_0|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|true_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_false_%7C_false|rs71574191_%7C_rs67841213_%7C_rs57681900|true_%7C_true_%7C_true|false_%7C_false_%7C_false|_%7C__%7C_|DIV_%7C_DIV_%7C_DIV|false_%7C_false_%7C_false] chr1 19408294 rs67232976 G GC 2309.93 PASS FUNCOTATION=[UBR4|hg19|chr1|19408294|19408295|INTRON||INS|-|-|C|g.chr1:19408294_19408295insC|ENST00000375254.3|-|||c.e103+227C>GC|||0.5125|TCTTCCCTGGCCCCATGTCT|UBR4_ENST00000375225.3_FRAME_SHIFT_INS_p.P3fs/UBR4_ENST00000375224.1_INTRON/UBR4_ENST00000375267.2_INTRON/UBR4_ENST00000375217.2_INTRON/UBR4_ENST00000375226.2_INTRON/UBR4_ENST00000543981.1_INTRON/UBR4_ENST00000429347.2_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.6306_%2C_0.3694|false|false|1||false|true|true|UBR4:23352|true|false|true|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|67232976|19408294|false|false|0|true|0|false|0.627653_%2C_0.372347|false|false|false|DIV|true|0x05010008000517013e000200|1|false|137|rs67232976] chr1 20501582 rs12139100 G A 275.25 PASS FUNCOTATION=[PLA2G2C|hg19|chr1|20501582|20501582|NONSENSE||SNP|G|G|A|g.chr1:20501582G>A|ENST00000429261.2|-|2|158|c.97C>T|c.(97-99)Cga>Tga|p.R33*|0.49875311720698257|AAGGCACTTCGCCCCGTGATG|PLA2G2C_ENST00000247992.5_NONSENSE_p.R36*/PLA2G2C_ENST00000495760.2_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.7598_%2C_0.2402|false|false|1||false|true|true|PLA2G2C:391013|true|true|false|true|true|false|false|false|false|false|false|false|true|false|false|false|false|false|false|true|12139100|20501582|false|false|0|true|0|false|0.791916_%2C_0.208084|false|false|false|SNV|true|0x05010000060517053f000100|1|false|120|rs12139100] @@ -192,30 +192,30 @@ chr1 22033385 . GA G 799.10 PASS FUNCOTATION=[USP48|hg19|chr1|22033386|22033386| chr1 23280024 . G GCAC 529.29 PASS FUNCOTATION=[LACTBL1|hg19|chr1|23280024|23280025|IN_FRAME_INS||INS|-|-|CAC|g.chr1:23280024_23280025insCAC|ENST00000426928.2|-|6|1153|c.1152_1153insGTG|c.(1150-1155)gtgctg>gtgGTGctg|p.384_385insV|0.765|CCAGCAGCAGCACCAGGCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|LACTBL1:646262|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|764403246|23280024|false|false|0|false|0|false||false|false|false|DIV|false|0x050000000005000002000200|1|false|144|rs764403246] chr1 23670803 rs12409193 G C 411.95 PASS FUNCOTATION=[HNRNPR|hg19|chr1|23670803|23670803|DE_NOVO_START_IN_FRAME||SNP|G|G|C|g.chr1:23670803G>C|ENST00000374616.3|-|1|||||0.683291770573566|TCCCCCCCCTGATGGACTGAG|HNRNPR_ENST00000374612.1_DE_NOVO_START_IN_FRAME/HNRNPR_ENST00000478691.1_DE_NOVO_START_OUT_FRAME|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.6534_%2C_0.3466|false|false|1||false|true|true|HNRNPR:10236|true|true|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|true|false|12409193|23670803|false|false|0|true|0|false|0.645099_%2C_0.354901|false|false|true|SNV|true|0x05010042000517053e000100|1|false|120|rs12409193] chr1 23966894 rs5773050 T TAAG 583.16 PASS FUNCOTATION=[MDS2|hg19|chr1|23966894|23966895|IN_FRAME_INS||INS|-|-|AAG|g.chr1:23966894_23966895insAAG|ENST00000374555.3|+|7|865|c.278_279insAAG|c.(277-279)gta>gtAAGa|p.93_94insR|0.4525|GTGGCTTTGTAAGAAGAAAA|MDS2_ENST00000477916.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|102_%7C_138|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|MDS2:259283_%7C_MDS2:259283|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.7232_%2C_0.2768_%7C_0.7232_%2C_0.2768|3072132_%7C_5773050|false_%7C_false|true_%7C_false|0x05010000000517003e000200_%7C_0x050000000005000002000200|true_%7C_false|false_%7C_false|23966894_%7C_23966902|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs3072132_%7C_rs5773050|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] -chr1 26608825 . TGGGGCCG T 2482.89 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608826|26608832|FRAME_SHIFT_DEL||DEL|GGGGCCG|GGGGCCG|-|g.chr1:26608826_26608832delGGGGCCG|ENST00000374222.1|-|16|1993|c.1521_1527delCGGCCCC|c.(1519-1527)cccggccccfs|p.G508fs|0.7002457002457002|GACAGGGACTGGGGCCGGGACCGGGAC|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.G508fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.G388fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.G475fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.G265fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.G475fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|752317296|26608826|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs752317296] -chr1 26608835 . ACCGGGACCGGGACTGGG A 2471.89 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608836|26608852|FRAME_SHIFT_DEL||DEL|CCGGGACCGGGACTGGG|CCGGGACCGGGACTGGG|-|g.chr1:26608836_26608852delCCGGGACCGGGACTGGG|ENST00000374222.1|-|16|1983|c.1501_1517delCCCAGTCCCGGTCCCGG|c.(1501-1518)cccagtcccggtcccggtfs|p.P501fs|0.6954436450839329|GGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.P501fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.P381fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.P468fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.P258fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.P468fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|757094832|26608836|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs757094832] -chr1 26608865 . ACC A 411.26 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608866|26608867|FRAME_SHIFT_DEL||DEL|CC|CC|-|g.chr1:26608866_26608867delCC|ENST00000374222.1|-|16|1953|c.1486_1487delGG|c.(1486-1488)ggtfs|p.G496fs|0.6865671641791045|GGGACCGGGACCGGGACTGGGG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.G496fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.G376fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.G463fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.G253fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.G463fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|764852231|26608866|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs764852231] -chr1 26608868 . GGGACTGGGGCCGGGACCGGGACCGGGAC G 372.26 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608869|26608896|FRAME_SHIFT_DEL||DEL|GGACTGGGGCCGGGACCGGGACCGGGAC|GGACTGGGGCCGGGACCGGGACCGGGAC|-|g.chr1:26608869_26608896delGGACTGGGGCCGGGACCGGGACCGGGAC|ENST00000374222.1|-|16|1950|c.1457_1484delGTCCCGGTCCCGGTCCCGGCCCCAGTCC|c.(1456-1485)tgtcccggtcccggtcccggccccagtcccfs|p.C486fs|0.6892523364485982|ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACAGGGACCAGG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.C486fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.C366fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.C453fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.C243fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.C453fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|757886085|26608869|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040002000200|1|false|144|rs757886085] -chr1 28800350 . CCAGAAA C 132.29 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800351|28800356|IN_FRAME_DEL||DEL|CAGAAA|CAGAAA|-|g.chr1:28800351_28800356delCAGAAA|ENST00000373836.3|+|6|1352|c.1139_1144delCAGAAA|c.(1138-1146)ccagaaatt>ctt|p.380_382PEI>L|0.5246305418719212|CAAGTTGTGCCAGAAATTGAGTTTCC|PHACTR4_ENST00000373839.3_IN_FRAME_DEL_p.370_372PEI>L/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 28800358 . TGAG T 130.68 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800359|28800361|IN_FRAME_DEL||DEL|GAG|GAG|-|g.chr1:28800359_28800361delGAG|ENST00000373836.3|+|6|1360|c.1147_1149delGAG|c.(1147-1149)gagdel|p.E383del|0.5260545905707196|GCCAGAAATTGAGTTTCCACCAT|PHACTR4_ENST00000373839.3_IN_FRAME_DEL_p.E373del/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 26608825 . TGGGGCCG T 2482.89 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608826|26608832|FRAME_SHIFT_DEL||DEL|GGGGCCG|GGGGCCG|-|g.chr1:26608826_26608832delGGGGCCG|ENST00000374222.1|-|16|1993_1999|c.1521_1527delCGGCCCC|c.(1519-1527)cccggccccfs|p.G508fs|0.7002457002457002|GACAGGGACTGGGGCCGGGACCGGGAC|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.G508fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.G388fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.G475fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.G265fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.G475fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|752317296|26608826|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs752317296] +chr1 26608835 . ACCGGGACCGGGACTGGG A 2471.89 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608836|26608852|FRAME_SHIFT_DEL||DEL|CCGGGACCGGGACTGGG|CCGGGACCGGGACTGGG|-|g.chr1:26608836_26608852delCCGGGACCGGGACTGGG|ENST00000374222.1|-|16|1983_1999|c.1501_1517delCCCAGTCCCGGTCCCGG|c.(1501-1518)cccagtcccggtcccggtfs|p.P501fs|0.6954436450839329|GGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.P501fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.P381fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.P468fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.P258fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.P468fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|757094832|26608836|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs757094832] +chr1 26608865 . ACC A 411.26 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608866|26608867|FRAME_SHIFT_DEL||DEL|CC|CC|-|g.chr1:26608866_26608867delCC|ENST00000374222.1|-|16|1953_1954|c.1486_1487delGG|c.(1486-1488)ggtfs|p.G496fs|0.6865671641791045|GGGACCGGGACCGGGACTGGGG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.G496fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.G376fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.G463fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.G253fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.G463fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|764852231|26608866|false|false|0|false|0|false||false|false|false|DIV|false|0x050000001205000002000200|1|false|144|rs764852231] +chr1 26608868 . GGGACTGGGGCCGGGACCGGGACCGGGAC G 372.26 PASS FUNCOTATION=[UBXN11|hg19|chr1|26608869|26608896|FRAME_SHIFT_DEL||DEL|GGACTGGGGCCGGGACCGGGACCGGGAC|GGACTGGGGCCGGGACCGGGACCGGGAC|-|g.chr1:26608869_26608896delGGACTGGGGCCGGGACCGGGACCGGGAC|ENST00000374222.1|-|16|1950_1977|c.1457_1484delGTCCCGGTCCCGGTCCCGGCCCCAGTCC|c.(1456-1485)tgtcccggtcccggtcccggccccagtcccfs|p.C486fs|0.6892523364485982|ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACAGGGACCAGG|UBXN11_ENST00000374221.3_FRAME_SHIFT_DEL_p.C486fs/UBXN11_ENST00000314675.7_FRAME_SHIFT_DEL_p.C366fs/UBXN11_ENST00000357089.4_FRAME_SHIFT_DEL_p.C453fs/UBXN11_ENST00000374223.1_FRAME_SHIFT_DEL_p.C243fs/UBXN11_ENST00000374217.2_FRAME_SHIFT_DEL_p.C453fs|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false||false|false|||false|false|false|UBXN11:91544|false|false|false|false|false|false|false|false|false|false|true|false|false|false|false|false|false|false|false|true|757886085|26608869|false|false|0|false|0|false||false|false|false|DIV|true|0x050000001205040002000200|1|false|144|rs757886085] +chr1 28800350 . CCAGAAA C 132.29 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800351|28800356|IN_FRAME_DEL||DEL|CAGAAA|CAGAAA|-|g.chr1:28800351_28800356delCAGAAA|ENST00000373836.3|+|6|1352_1357|c.1139_1144delCAGAAA|c.(1138-1146)ccagaaatt>ctt|p.380_382PEI>L|0.5246305418719212|CAAGTTGTGCCAGAAATTGAGTTTCC|PHACTR4_ENST00000373839.3_IN_FRAME_DEL_p.370_372PEI>L/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 28800358 . TGAG T 130.68 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800359|28800361|IN_FRAME_DEL||DEL|GAG|GAG|-|g.chr1:28800359_28800361delGAG|ENST00000373836.3|+|6|1360_1362|c.1147_1149delGAG|c.(1147-1149)gagdel|p.E383del|0.5260545905707196|GCCAGAAATTGAGTTTCCACCAT|PHACTR4_ENST00000373839.3_IN_FRAME_DEL_p.E373del/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 28800364 . T TTAATGATACGG 174.58 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800364|28800365|FRAME_SHIFT_INS||INS|-|-|TAATGATACGG|g.chr1:28800364_28800365insTAATGATACGG|ENST00000373836.3|+|6|1366|c.1152_1153insTAATGATACGG|c.(1153-1155)ccafs|p.P385fs|0.525|AATTGAGTTTCCACCATCCT|PHACTR4_ENST00000373839.3_FRAME_SHIFT_INS_p.P375fs/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 28800370 . AT A 200.53 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800371|28800371|FRAME_SHIFT_DEL||DEL|T|T|-|g.chr1:28800371delT|ENST00000373836.3|+|6|1372|c.1159delT|c.(1159-1161)tccfs|p.S387fs|0.5236907730673317|GTTTCCACCATCCTTAGATCT|PHACTR4_ENST00000373839.3_FRAME_SHIFT_DEL_p.S377fs/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 28800375 . T G 213.53 PASS FUNCOTATION=[PHACTR4|hg19|chr1|28800375|28800375|NONSENSE||SNP|T|T|G|g.chr1:28800375T>G|ENST00000373836.3|+|6|1377|c.1163T>G|c.(1162-1164)tTa>tGa|p.L388*|0.5211970074812967|CCACCATCCTTAGATCTACAC|PHACTR4_ENST00000373839.3_NONSENSE_p.L378*/PHACTR4_ENST00000493669.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 31882582 rs4012494 G GGCCTCA 1419.16 PASS FUNCOTATION=[SERINC2|hg19|chr1|31882582|31882583|FIVE_PRIME_UTR||INS|-|-|GCCTCA|g.chr1:31882582_31882583insGCCTCA|ENST00000373710.1|+|1|||||0.5025|ATAAGGGATGGCCCTGCTCT|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true_%7C_true|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|108_%7C_130|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|SERINC2:347735_%7C_SERINC2:347735|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|true_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.4065_%2C_0.5935_%7C_0.4065_%2C_0.5935|4012494_%7C_6143179|false_%7C_false|true_%7C_false|0x05010042000517012e000200_%7C_0x050100420005000102000200|true_%7C_false|false_%7C_false|31882582_%7C_31882585|0_%7C_0|false_%7C_false|true_%7C_false|true_%7C_true|false_%7C_false|true_%7C_true|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs4012494_%7C_rs6143179|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 31905889 rs3050461 A ACAG 3632.73 PASS FUNCOTATION=[SERINC2|hg19|chr1|31905889|31905890|IN_FRAME_INS||INS|-|-|CAG|g.chr1:31905889_31905890insCAG|ENST00000373709.3|+|9|1239|c.1089_1090insCAG|c.(1090-1092)cag>CAGcag|p.363_364insQ|0.6025|AGACGCCACACAGCAGCAGC|SERINC2_ENST00000373710.1_IN_FRAME_INS_p.372_373insQ/SERINC2_ENST00000536384.1_IN_FRAME_INS_p.367_368insQ/SERINC2_ENST00000536859.1_IN_FRAME_INS_p.367_368insQ/SERINC2_ENST00000491976.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|102_%7C_126|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|SERINC2:347735_%7C_SERINC2:347735|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|true_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.261_%2C_0.739_%7C_0.261_%2C_0.739|3050461_%7C_5773362|false_%7C_false|true_%7C_false|0x05010000000517002e000200_%7C_0x050100000005000102000200|true_%7C_false|false_%7C_false|31905889_%7C_31905904|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_true|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs3050461_%7C_rs5773362|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 36184975 rs7521021 G A 3135.69 PASS FUNCOTATION=[C1orf216|hg19|chr1|36184975|36184975|DE_NOVO_START_OUT_FRAME||SNP|G|G|A|g.chr1:36184975G>A|ENST00000270815.4|-|1|||||0.5461346633416458|CCTAGATCACGTTCGTTCCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.02416_%2C_0.9758|false|false|1||false|true|false|C1orf216:127703|true|true|false|true|true|false|false|false|false|false|false|false|false|false|false|false|false|false|true|false|7521021|36184975|false|false|0|true|0|false|0.025929_%2C_0.974071|false|false|false|SNV|true|0x05010002000515053f000100|1|false|116|rs7521021] -chr1 36643700 rs141305015 GAGA G 909.25 PASS FUNCOTATION=[MAP7D1|hg19|chr1|36643701|36643703|IN_FRAME_DEL||DEL|AGA|AGA|-|g.chr1:36643701_36643703delAGA|ENST00000373151.2|+|9|1822|c.1607_1609delAGA|c.(1606-1611)gagaag>gag|p.K537del|0.6972704714640199|GCCAGTAACGAGAAGGAGTCAGC|MAP7D1_ENST00000373150.4_IN_FRAME_DEL_p.K505del/MAP7D1_ENST00000316156.4_IN_FRAME_DEL_p.K500del/MAP7D1_ENST00000373148.4_IN_FRAME_DEL_p.K83del||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|134_%7C_102|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|MAP7D1:55700_%7C_MAP7D1:55700|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|0.973178_%2C_0.0268219_%7C_|false_%7C_false|false_%7C_false|0.9355_%2C_0.0645_%7C_0.9355_%2C_0.0645|141305015_%7C_3045695|false_%7C_false|false_%7C_true|0x05000000000515003e000200_%7C_0x050100000005000002000200|false_%7C_false|false_%7C_false|36643701_%7C_36643703|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs141305015_%7C_rs3045695|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] +chr1 36643700 rs141305015 GAGA G 909.25 PASS FUNCOTATION=[MAP7D1|hg19|chr1|36643701|36643703|IN_FRAME_DEL||DEL|AGA|AGA|-|g.chr1:36643701_36643703delAGA|ENST00000373151.2|+|9|1822_1824|c.1607_1609delAGA|c.(1606-1611)gagaag>gag|p.K537del|0.6972704714640199|GCCAGTAACGAGAAGGAGTCAGC|MAP7D1_ENST00000373150.4_IN_FRAME_DEL_p.K505del/MAP7D1_ENST00000316156.4_IN_FRAME_DEL_p.K500del/MAP7D1_ENST00000373148.4_IN_FRAME_DEL_p.K83del||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|134_%7C_102|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|MAP7D1:55700_%7C_MAP7D1:55700|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|0.973178_%2C_0.0268219_%7C_|false_%7C_false|false_%7C_false|0.9355_%2C_0.0645_%7C_0.9355_%2C_0.0645|141305015_%7C_3045695|false_%7C_false|false_%7C_true|0x05000000000515003e000200_%7C_0x050100000005000002000200|false_%7C_false|false_%7C_false|36643701_%7C_36643703|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs141305015_%7C_rs3045695|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 40131838 . T TC 48.29 PASS FUNCOTATION=[NT5C1A|hg19|chr1|40131838|40131839|FRAME_SHIFT_INS||INS|-|-|C|g.chr1:40131838_40131839insC|ENST00000235628.1|-|2|206|c.205_206insG|c.(205-207)cagfs|p.Q69fs|0.565|GTGTAGATCTGCTGCTCCTC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 40131850 . T TA 48.29 PASS FUNCOTATION=[NT5C1A|hg19|chr1|40131850|40131851|FRAME_SHIFT_INS||INS|-|-|A|g.chr1:40131850_40131851insA|ENST00000235628.1|-|2|194|c.193_194insT|c.(193-195)gacfs|p.D65fs|0.555|TGCTCCTCGTCCATGCGAAA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr1 41847872 . G GGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC 3817.87 PASS FUNCOTATION=[FOXO6|hg19|chr1|41847872|41847873|FRAME_SHIFT_INS||INS|-|-|GCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC|g.chr1:41847872_41847873insGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC|ENST00000372591.1|+|2|1008|c.999_1000insGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC|c.(1000-1002)gccfs|p.Q337fs|0.8125|CGGGCCGCGGGCCCGCGCCC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 44596379 rs34057178 CCAA C 850.25 PASS FUNCOTATION=[KLF17|hg19|chr1|44596380|44596382|IN_FRAME_DEL||DEL|CAA|CAA|-|g.chr1:44596380_44596382delCAA|ENST00000372299.3|+|3|1179|c.1122_1124delCAA|c.(1120-1125)gccaac>gcc|p.N375del|0.5012406947890818|ACCCACAGGCCAACAACAACAAT|KLF17_ENST00000476802.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|1_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|126_%7C_137|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|KLF17:128209_%7C_KLF17:128209|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|0.857614_%2C_0.142386_%7C_|false_%7C_false|false_%7C_false|0.7698_%2C_0.2302_%7C_0.7698_%2C_0.2302|34057178_%7C_200059598|false_%7C_false|false_%7C_false|0x05000000000517003e000240_%7C_0x050000000005000002000200|true_%7C_false|false_%7C_false|44596380_%7C_44596388|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs34057178_%7C_rs200059598|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] +chr1 44596379 rs34057178 CCAA C 850.25 PASS FUNCOTATION=[KLF17|hg19|chr1|44596380|44596382|IN_FRAME_DEL||DEL|CAA|CAA|-|g.chr1:44596380_44596382delCAA|ENST00000372299.3|+|3|1179_1181|c.1122_1124delCAA|c.(1120-1125)gccaac>gcc|p.N375del|0.5012406947890818|ACCCACAGGCCAACAACAACAAT|KLF17_ENST00000476802.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|1_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|126_%7C_137|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|KLF17:128209_%7C_KLF17:128209|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|0.857614_%2C_0.142386_%7C_|false_%7C_false|false_%7C_false|0.7698_%2C_0.2302_%7C_0.7698_%2C_0.2302|34057178_%7C_200059598|false_%7C_false|false_%7C_false|0x05000000000517003e000240_%7C_0x050000000005000002000200|true_%7C_false|false_%7C_false|44596380_%7C_44596388|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs34057178_%7C_rs200059598|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 47080679 rs6671527 G A 1927.94 PASS FUNCOTATION=[MOB3C|hg19|chr1|47080679|47080679|NONSENSE||SNP|G|G|A|g.chr1:47080679G>A|ENST00000271139.8|-|1|127|c.70C>T|c.(70-72)Cga>Tga|p.R24*|0.5087281795511222|CCGACTCTTCGACTTCTCACC|MOB3C_ENST00000371940.1_FIVE_PRIME_UTR/MOB3C_ENST00000319928.3_INTRON/MKNK1_ENST00000545730.1_INTRON/MOB3C_ENST00000477318.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.3578_%2C_0.6422_%2C_.|false|false|1||false|true|false|MOB3C:148932|true|true|true|true|true|false|false|false|false|false|false|true|true|false|false|false|false|false|false|true|6671527|47080679|false|false|0|true|0|false|0.472526_%2C_0.527474_%2C_.|false|false|false|SNV|true|0x050100080e0515053f000101|1|false|116|rs6671527] chr1 47904668 rs71053113 T TCCGCAC 4677.73 PASS FUNCOTATION=[FOXD2|hg19|chr1|47904668|47904669|IN_FRAME_INS||INS|-|-|CCGCAC|g.chr1:47904668_47904669insCCGCAC|ENST00000334793.5|+|1|2980|c.861_862insCCGCAC|c.(862-864)ccg>CCGCACccg|p.287_288insPH|0.795|GGCCCCGCATCCGCACCCGC|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|102_%7C_130|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|FOXD2:2306_%7C_FOXD2:2306|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|true_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.03554_%2C_0.9645_%2C_._%7C_0.03554_%2C_0.9645|3046924_%7C_71053113|false_%7C_false|true_%7C_true|0x05010000000515003e000200_%7C_0x050100000005000102000200|false_%7C_false|false_%7C_false|47904668_%7C_47904686|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_true|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs3046924_%7C_rs71053113|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 48569478 . C CTGTG 426.29 PASS FUNCOTATION=[AL109659.1|hg19|chr1|48569478|48569479|FRAME_SHIFT_INS||INS|-|-|TGTG|g.chr1:48569478_48569479insTGTG|ENST00000601108.1|+|1|173|c.173_174insTGTG|c.(172-174)tctfs|p.I65fs|0.465|GGTGTGTGTCTGTGTGTGTG|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|138_%7C_149|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|SKINT1L:391037_%7C_SKINT1L:391037|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.9379_%2C_0.03135_%2C_0.03075_%7C_0.9379_%2C_0.03135_%2C_0.03075|373596514_%7C_879571472|false_%7C_false|false_%7C_false|0x050000080005140026000200_%7C_0x050000080005000002000200|false_%7C_false|false_%7C_false|48569478_%7C_48569497|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|true_%7C_true|_%7C_|true_%7C_false|rs373596514_%7C_rs879571472|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 48708228 rs850763 G T 386.25 PASS FUNCOTATION=[SLC5A9|hg19|chr1|48708228|48708228|NONSENSE||SNP|G|G|T|g.chr1:48708228G>T|ENST00000438567.2|+|13|1829|c.1777G>T|c.(1777-1779)Gag>Tag|p.E593*|0.5835411471321695|GCCAGCCGGGGAGTGCCCTGC|SLC5A9_ENST00000236495.5_NONSENSE_p.E618*/SLC5A9_ENST00000533824.1_NONSENSE_p.E614*/SLC5A9_ENST00000471020.1_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.8862_%2C_0.1138|false|false|1||false|true|false|SLC5A9:200010|true|true|false|true|true|false|false|false|false|false|false|false|true|false|false|false|false|false|false|true|850763|48708228|true|false|0|true|0|false|0.859228_%2C_0.140772|false|false|false|SNV|true|0x050100000605150537000100|1|false|86|rs850763] -chr1 50884773 rs4027495 CCGGCGG C 1244.13 PASS FUNCOTATION=[DMRTA2|hg19|chr1|50884774|50884779|IN_FRAME_DEL||DEL|CGGCGG|CGGCGG|-|g.chr1:50884774_50884779delCGGCGG|ENST00000404795.3|-|3|1586|c.1187_1192delCCGCCG|c.(1186-1194)gccgccggg>ggg|p.AA396del|0.7807881773399015|CCAGGCCCCCCGGCGGCGGCGGCGGC|DMRTA2_ENST00000418121.1_IN_FRAME_DEL_p.AA396del||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|144_%7C_108|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|DMRTA2:63950_%7C_DMRTA2:63950|_%7C_|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|761537995_%7C_4027495|false_%7C_false|false_%7C_false|0x050000000005000002000200_%7C_0x050000000005000002000200|false_%7C_false|false_%7C_false|50884774_%7C_50884792|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|rs761537995_%7C_rs4027495|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] +chr1 50884773 rs4027495 CCGGCGG C 1244.13 PASS FUNCOTATION=[DMRTA2|hg19|chr1|50884774|50884779|IN_FRAME_DEL||DEL|CGGCGG|CGGCGG|-|g.chr1:50884774_50884779delCGGCGG|ENST00000404795.3|-|3|1586_1591|c.1187_1192delCCGCCG|c.(1186-1194)gccgccggg>ggg|p.AA396del|0.7807881773399015|CCAGGCCCCCCGGCGGCGGCGGCGGC|DMRTA2_ENST00000418121.1_IN_FRAME_DEL_p.AA396del||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|144_%7C_108|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|DMRTA2:63950_%7C_DMRTA2:63950|_%7C_|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|761537995_%7C_4027495|false_%7C_false|false_%7C_false|0x050000000005000002000200_%7C_0x050000000005000002000200|false_%7C_false|false_%7C_false|50884774_%7C_50884792|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|rs761537995_%7C_rs4027495|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 50884775 . G *,GGCA 1910.68 PASS FUNCOTATION=[Unknown|hg19|chr1|50884775|50884775|COULD_NOT_DETERMINE||NA|G|G|*||ENST00000404795.3|+||||||0.7805486284289277|CAGGCCCCCCGGCGGCGGCGG|null_ENST00000418121.1_COULD_NOT_DETERMINE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||],[DMRTA2|hg19|chr1|50884775|50884776|IN_FRAME_INS||INS|-|-|GCA|g.chr1:50884775_50884776insGCA|ENST00000404795.3|-|3|1584|c.1190_1191insTGC|c.(1189-1191)gcc>gcTGCc|p.397_398insA|0.78|AGGCCCCCCGGCGGCGGCGG|DMRTA2_ENST00000418121.1_IN_FRAME_INS_p.397_398insA|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 52306063 rs35723519 ATCT A 1359.12 PASS FUNCOTATION=[NRD1|hg19|chr1|52306064|52306066|IN_FRAME_DEL||DEL|TCT|TCT|-|g.chr1:52306064_52306066delTCT|ENST00000354831.7|-|2|655|c.462_464delAGA|c.(460-465)gaagat>gat|p.E154del|0.36476426799007444|TTCATCATCATCTTCTTCTTCTT|NRD1_ENST00000352171.7_IN_FRAME_DEL_p.E154del/NRD1_ENST00000539524.1_IN_FRAME_DEL_p.E22del/NRD1_ENST00000544028.1_IN_FRAME_DEL_p.E22del/NRD1_ENST00000485608.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|126_%7C_129|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|NRD1:4898_%7C_NRDC:4898_%7C_NRD1:4898_%7C_NRDC:4898|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.4383_%2C_0.5617_%7C_0.4383_%2C_0.5617|35723519_%7C_60220085|false_%7C_false|false_%7C_false|0x05000000000517003e000200_%7C_0x050100000005000102000200|true_%7C_false|false_%7C_false|52306064_%7C_52306075|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_true|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs35723519_%7C_rs60220085|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] +chr1 52306063 rs35723519 ATCT A 1359.12 PASS FUNCOTATION=[NRD1|hg19|chr1|52306064|52306066|IN_FRAME_DEL||DEL|TCT|TCT|-|g.chr1:52306064_52306066delTCT|ENST00000354831.7|-|2|655_657|c.462_464delAGA|c.(460-465)gaagat>gat|p.E154del|0.36476426799007444|TTCATCATCATCTTCTTCTTCTT|NRD1_ENST00000352171.7_IN_FRAME_DEL_p.E154del/NRD1_ENST00000539524.1_IN_FRAME_DEL_p.E22del/NRD1_ENST00000544028.1_IN_FRAME_DEL_p.E22del/NRD1_ENST00000485608.1_INTRON||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|true_%7C_false|126_%7C_129|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|NRD1:4898_%7C_NRDC:4898_%7C_NRD1:4898_%7C_NRDC:4898|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_true|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.4383_%2C_0.5617_%7C_0.4383_%2C_0.5617|35723519_%7C_60220085|false_%7C_false|false_%7C_false|0x05000000000517003e000200_%7C_0x050100000005000102000200|true_%7C_false|false_%7C_false|52306064_%7C_52306075|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_true|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs35723519_%7C_rs60220085|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 53925373 . G GCCGCCC 637.29 PASS FUNCOTATION=[DMRTB1|hg19|chr1|53925373|53925374|IN_FRAME_INS||INS|-|-|CCGCCC|g.chr1:53925373_53925374insCCGCCC|ENST00000371445.3|+|1|302|c.247_248insCCGCCC|c.(247-249)gcc>gCCGCCCcc|p.83_84insAP|0.7475|GCTGCGGCCGCCGCCCCCGC|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false|false_%7C_false|0_%7C_0|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|true_%7C_false|142_%7C_144|false_%7C_false|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|DMRTB1:63948_%7C_DMRTB1:63948|_%7C_|false_%7C_false|1_%7C_1|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|0.8926_%2C_0.1074_%7C_0.8926_%2C_0.1074|575081928_%7C_766482978|false_%7C_false|false_%7C_false|0x050000000005150026000200_%7C_0x050000000005000002000200|false_%7C_false|false_%7C_false|53925373_%7C_53925379|0_%7C_0|false_%7C_false|true_%7C_false|false_%7C_false|false_%7C_false|false_%7C_false|_%7C_|false_%7C_false|false_%7C_false|_%7C_|true_%7C_false|rs575081928_%7C_rs766482978|true_%7C_true|false_%7C_false|DIV_%7C_DIV|_%7C_|false_%7C_false] chr1 55182300 rs1147990 T A 2208.94 PASS FUNCOTATION=[TTC4|hg19|chr1|55182300|55182300|MISSENSE||SNP|T|T|A|g.chr1:55182300T>A|ENST00000371281.3|+|2|226|c.139T>A|c.(139-141)Tcg>Acg|p.S47T|0.3915211970074813|CCTATTTATGTCGAGAGCGCC|TTC4_ENST00000371284.5_INTRON/MROH7-TTC4_ENST00000414150.2_NONSENSE_p.C1282*|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||true|false|0.3317_%2C_0.6683|false|false|1||false|true|false|TTC4:7268_%7C_MROH7-TTC4:100527960|true|true|false|true|true|false|false|false|false|false|false|true|false|false|false|true|true|false|false|true|1147990|55182300|true|false|0|true|0|false|0.448314_%2C_0.551686|false|false|false|SNV|true|0x050128000a0515053f000101|1|false|87|rs1147990] chr1 55505552 rs113330492 A ACTG 1612.14 PASS FUNCOTATION=[PCSK9|hg19|chr1|55505552|55505553|IN_FRAME_INS||INS|-|-|CTG|g.chr1:55505552_55505553insCTG|ENST00000302118.5|+|1|332|c.42_43insCTG|c.(43-45)ctg>CTGctg|p.14_15insL|0.7075|GCCGCTGCCACTGCTGCTGC|PCSK9_ENST00000452118.2_IN_FRAME_INS_p.14_15insL||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false_%7C_false_%7C_false|false_%7C_false_%7C_false|0_%7C_0_%7C_0|false_%7C_false_%7C_false|false_%7C_false_%7C_true|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|127_%7C_132_%7C_126|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|1_%7C_1_%7C_1|false_%7C_false_%7C_false|_%7C__%7C_|PCSK9:255738_%7C_PCSK9:255738_%7C_PCSK9:255738|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_true_%7C_true|false_%7C_false_%7C_true|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|false_%7C_false_%7C_false|_%7C__%7C_|45454392_%7C_113330492_%7C_35574083|false_%7C_false_%7C_false|false_%7C_false_%7C_false|0x050000020005070102000200_%7C_0x050100020005000102000200_%7C_0x050168020005040102100200|true_%7C_false_%7C_false|false_%7C_false_%7C_false|55505554_%7C_55505563_%7C_55505575|0_%7C_0_%7C_1|false_%7C_false_%7C_false|true_%7C_false_%7C_false|false_%7C_false_%7C_false|true_%7C_true_%7C_true|_%7C__%7C_|true_%7C_true_%7C_true|false_%7C_false_%7C_false|_%7C__%7C_|false_%7C_false_%7C_false|true_%7C_false_%7C_true|rs45454392_%7C_rs113330492_%7C_rs35574083|true_%7C_true_%7C_true|false_%7C_false_%7C_false|_%7C__%7C_|DIV_%7C_DIV_%7C_DIV|false_%7C_false_%7C_true] diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.maf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.maf index ce4302e375b..08847323073 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.maf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.maf @@ -3422,12 +3422,12 @@ ## source=GenomicsDBImport ## source=GenotypeGVCFs ## source=VariantFiltration -## GATKCommandLine= +## GATKCommandLine= ## source=Funcotator -## Funcotator 0.0.5 | Date 20184130T024128 | Gencode 28 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 90_38 | Gencode_XRefSeq 90_38 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 +## Funcotator 0.0.5 | Date 20184831T034826 | Gencode 28 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 90_38 | Gencode_XRefSeq 90_38 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_28 _hugoSymbol Gencode_28 _ncbiBuild Gencode_28 _chromosome Gencode_28 _start Gencode_28 _end Gencode_28 _variantClassification Gencode_28 _secondaryVariantClassification Gencode_28 _variantType Gencode_28 _refAllele Gencode_28 _tumorSeqAllele1 Gencode_28 _tumorSeqAllele2 Gencode_28 _genomeChange Gencode_28 _annotationTranscript Gencode_28 _transcriptStrand Gencode_28 _transcriptExon Gencode_28 _transcriptPos Gencode_28 _cDnaChange Gencode_28 _codonChange Gencode_28 _proteinChange Gencode_28 _gcContent Gencode_28 _referenceContext Gencode_28 _otherTranscripts Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Simple_Uniprot_alt_uniprot_accessions dbSNP_AC dbSNP_AF dbSNP_AN dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DP dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD AC AF AN BaseQRankSum ClippingRankSum DB DP DS END ExcessHet FS HaplotypeScore InbreedingCoeff MLEAC MLEAF MQ MQRankSum NEGATIVE_TRAIN_SITE POSITIVE_TRAIN_SITE QD RAW_MQ ReadPosRankSum SOR VQSLOD culprit -__UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ENAH hg38 chr1 225519331 225519349 IN_FRAME_DEL DEL ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGC A g.chr1:225519332_225519349delTCCAGGCGTTCCTGCCGC ENST00000366844.7 - 5 1121 c.651_668delGCGGCAGGAACGCCTGGA c.(649-669)gagcggcaggaacgcctggat>gat p.ERQERL217del 0.5382775119617225 CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT ENAH_ENST00000635051.1_IN_FRAME_DEL_p.ERQERL221del/ENAH_ENST00000366843.6_IN_FRAME_DEL_p.ERQERL217del false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false -__UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ENAH hg38 chr1 225519331 225519349 IN_FRAME_INS INS ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGCTCCAGGCGTTCCTGCCGC g.chr1:225519331_225519332insTCCAGGCGTTCCTGCCGC ENST00000366844.7 - 5 1121 c.650_651insGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGA c.(649-669)gagcggcaggaacgcctggat>gaGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAt p.217_224insRLERQE 0.5382775119617225 CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT ENAH_ENST00000635051.1_IN_FRAME_INS_p.221_228insRLERQE/ENAH_ENST00000366843.6_IN_FRAME_INS_p.217_224insRLERQE false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +__UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ENAH hg38 chr1 225519331 225519349 IN_FRAME_DEL DEL ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGC A g.chr1:225519332_225519349delTCCAGGCGTTCCTGCCGC ENST00000366844.7 - 5 1121_1138 c.651_668delGCGGCAGGAACGCCTGGA c.(649-669)gagcggcaggaacgcctggat>gat p.ERQERL217del 0.5382775119617225 CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT ENAH_ENST00000635051.1_IN_FRAME_DEL_p.ERQERL221del/ENAH_ENST00000366843.6_IN_FRAME_DEL_p.ERQERL217del false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false +__UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ ENAH hg38 chr1 225519331 225519349 IN_FRAME_INS INS ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGCTCCAGGCGTTCCTGCCGC g.chr1:225519331_225519332insTCCAGGCGTTCCTGCCGC ENST00000366844.7 - 5 1121_1138 c.650_651insGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGA c.(649-669)gagcggcaggaacgcctggat>gaGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAt p.217_224insRLERQE 0.5382775119617225 CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT ENAH_ENST00000635051.1_IN_FRAME_INS_p.221_228insRLERQE/ENAH_ENST00000366843.6_IN_FRAME_INS_p.217_224insRLERQE false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ PCSK5 hg38 chr9 76175291 76175296 INTRON DEL CGAATA CGAATA C g.chr9:76175292_76175296delGAATA ENST00000376752.8 + c.e14+162CGAATA>C 0.3851851851851852 GAATCGAATCGAATAGAATAGAATA PCSK5_ENST00000376767.7_FRAME_SHIFT_DEL_p.E690fs/PCSK5_ENST00000545128.5_INTRON false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ PCSK5 hg38 chr9 76175291 76175296 INTRON INS CGAATA CGAATA CGAATAGAATA g.chr9:76175291_76175292insGAATA ENST00000376752.8 + c.e14+162CGAATA>CGAATAGAATA 0.3851851851851852 GAATCGAATCGAATAGAATAGAATA PCSK5_ENST00000376767.7_NONSTOP_p.*692fs/PCSK5_ENST00000545128.5_INTRON false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ + __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ CCDC40 hg38 chr17 80090386 80090449 INTRON DEL CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA C g.chr17:80090387_80090449delAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA ENST00000397545.8 + c.e17+502CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA>C 0.572354211663067 GGACACACACAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACAAGCACGTGCA CCDC40_ENST00000374877.7_COULD_NOT_DETERMINE false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf index fd5e76bcf56..02a0bc4e0e6 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf @@ -22,7 +22,7 @@ ##GATKCommandLine.HaplotypeCaller= ##GATKCommandLine= ##GATKCommandLine= -##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##GATKCommandLine= ##GATKCommandLine= 54.69 --filter-name ExcessHet --variant /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-GenotypeGVCFs/shard-0/output.vcf.gz --cluster-size 3 --cluster-window-size 0 --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 5:33:28 PM UTC"> @@ -3425,7 +3425,7 @@ ##source=GenotypeGVCFs ##source=VariantFiltration #CHROM POS ID REF ALT QUAL FILTER INFO -chr1 225519331 rs71170086 ATCCAGGCGTTCCTGCCGC A . PASS FUNCOTATION=[ENAH|hg38|chr1|225519332|225519349|IN_FRAME_DEL||DEL|TCCAGGCGTTCCTGCCGC|TCCAGGCGTTCCTGCCGC|-|g.chr1:225519332_225519349delTCCAGGCGTTCCTGCCGC|ENST00000366844.7|-|5|1121|c.651_668delGCGGCAGGAACGCCTGGA|c.(649-669)gagcggcaggaacgcctggat>gat|p.ERQERL217del|0.5382775119617225|CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT|ENAH_ENST00000635051.1_IN_FRAME_DEL_p.ERQERL221del/ENAH_ENST00000366843.6_IN_FRAME_DEL_p.ERQERL217del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] -chr1 225519331 rs71170086 ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGCTCCAGGCGTTCCTGCCGC . PASS FUNCOTATION=[ENAH|hg38|chr1|225519331|225519332|IN_FRAME_INS||INS|-|-|TCCAGGCGTTCCTGCCGC|g.chr1:225519331_225519332insTCCAGGCGTTCCTGCCGC|ENST00000366844.7|-|5|1121|c.650_651insGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGA|c.(649-669)gagcggcaggaacgcctggat>gaGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAt|p.217_224insRLERQE|0.5382775119617225|CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT|ENAH_ENST00000635051.1_IN_FRAME_INS_p.221_228insRLERQE/ENAH_ENST00000366843.6_IN_FRAME_INS_p.217_224insRLERQE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 225519331 rs71170086 ATCCAGGCGTTCCTGCCGC A . PASS FUNCOTATION=[ENAH|hg38|chr1|225519332|225519349|IN_FRAME_DEL||DEL|TCCAGGCGTTCCTGCCGC|TCCAGGCGTTCCTGCCGC|-|g.chr1:225519332_225519349delTCCAGGCGTTCCTGCCGC|ENST00000366844.7|-|5|1121_1138|c.651_668delGCGGCAGGAACGCCTGGA|c.(649-669)gagcggcaggaacgcctggat>gat|p.ERQERL217del|0.5382775119617225|CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT|ENAH_ENST00000635051.1_IN_FRAME_DEL_p.ERQERL221del/ENAH_ENST00000366843.6_IN_FRAME_DEL_p.ERQERL217del|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] +chr1 225519331 rs71170086 ATCCAGGCGTTCCTGCCGC ATCCAGGCGTTCCTGCCGCTCCAGGCGTTCCTGCCGC . PASS FUNCOTATION=[ENAH|hg38|chr1|225519331|225519332|IN_FRAME_INS||INS|-|-|TCCAGGCGTTCCTGCCGC|g.chr1:225519331_225519332insTCCAGGCGTTCCTGCCGC|ENST00000366844.7|-|5|1121_1138|c.650_651insGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGA|c.(649-669)gagcggcaggaacgcctggat>gaGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAt|p.217_224insRLERQE|0.5382775119617225|CCTCTCCCGATCCAGGCGTTCCTGCCGCTCCAGGCGTT|ENAH_ENST00000635051.1_IN_FRAME_INS_p.221_228insRLERQE/ENAH_ENST00000366843.6_IN_FRAME_INS_p.217_224insRLERQE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr9 76175291 . CGAATA C,CGAATAGAATA . PASS FUNCOTATION=[PCSK5|hg38|chr9|76175292|76175296|INTRON||DEL|GAATA|GAATA|-|g.chr9:76175292_76175296delGAATA|ENST00000376752.8|+|||c.e14+162CGAATA>C|||0.3851851851851852|GAATCGAATCGAATAGAATAGAATA|PCSK5_ENST00000376767.7_FRAME_SHIFT_DEL_p.E690fs/PCSK5_ENST00000545128.5_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||],[PCSK5|hg38|chr9|76175291|76175292|INTRON||INS|-|-|GAATA|g.chr9:76175291_76175292insGAATA|ENST00000376752.8|+|||c.e14+162CGAATA>CGAATAGAATA|||0.3851851851851852|GAATCGAATCGAATAGAATAGAATA|PCSK5_ENST00000376767.7_NONSTOP_p.*692fs/PCSK5_ENST00000545128.5_INTRON|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] chr17 80090386 rs71163918 CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA C . PASS FUNCOTATION=[CCDC40|hg38|chr17|80090387|80090449|INTRON||DEL|AGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA|AGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA|-|g.chr17:80090387_80090449delAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA|ENST00000397545.8|+|||c.e17+502CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA>C|||0.572354211663067|GGACACACACAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACAAGCACGTGCA|CCDC40_ENST00000374877.7_COULD_NOT_DETERMINE|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false||false|false|||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||] diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java index bc4400c5992..dac5e12d937 100644 --- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java @@ -395,7 +395,7 @@ public static void assertEqualVariants(final List v1, final List for (int i = 0; i < v1.size(); i++) { if (! v1.get(i).toStringDecodeGenotypes().equals(v2.get(i).toStringDecodeGenotypes())){ - logger.error("Variant Comparison Error: " + "different element (compared by toStringDecodeGenotypes) " + i + ":\n" + v1.get(i) + "\n" + v2.get(i)); + logger.error("Variant Comparison Error: different element (compared by toStringDecodeGenotypes) " + i + ":\n" + v1.get(i) + "\n" + v2.get(i)); passed = false; ++numFailed; }