-
Notifications
You must be signed in to change notification settings - Fork 23
Deprecated exon and intron position notations
The current version of Mutalyzer supports deprecated (non-HGVS) notations for exon positions and exon ranges using exon numbers and positions in introns. These notations make use of now forbidden exon- and intron numbers.
In some cases the start- and end positions of an exon are needed to describe a
variant that encompasses the entire exon. For these cases, the EX notation
can be used.
We write EXn to denote the range (a, b), where a is the start of exon
n and b is the end of exon n.
For example, the range denoted by EX2 in the variant description
NM_002001.2:c.EX2del is equal to the range -59_55 in the description
NM_002001.2:c.-59_55del.
Additionally, a range of exons can be used to describe ranges covering multiple exons.
We write EXn-m to denote the range (a, b), where a is the start of
exon n and b is the end of exon m.
For example, the range denoted by EX2-4 in the variant description
NM_002001.2:c.EX2-4del is equal to the range -59_331 in the description
NM_002001.2:c.-59_331del.
Intronic positions are given relative to the start- or end position of an exon.
If these latter positions are not known, the IVS notation can be used.
We write IVSn+m to denote the position that is m positions downstream
of the start of intron n. Similartly, we write IVSn-m to denote the
position that is m positions upstream of the end of intron n.
For example, the position denoted by IVS2+3 in the variant description
NG_012337.1(SDHD_v001):c.IVS2+3del is equal to the position 169+3 in the
description NG_012337.1(SDHD_v001):c.169+3del. Likewise, the position
IVS2-3 in the description NG_012337.1(SDHD_v001):c.IVS2-3del equals the
position 170-3 in the description NG_012337.1(SDHD_v001):c.170-3del.
Please note that Mutalyzer has no knowledge of exon names, it simply interprets an exon- or intron number as an ordinal. So "exon 1b" or names like this are not supported, this may give unexpected results, especially for transcripts for which an exon was added at some point.
Please note that these notations are no longer used because exon numbering is explicitly prohibited by the HGVS and therefore will be removed from Mutalyzer at some point in the future.