Open for comments - SVD-WG003


Published: May 14, 2015
Closes:  July 16, 2015


Proposal


SVD-WG003 suggests to extend the current HGVS recommendations for the description of sequence variants with the proposal below. Comments can be sent to the HGVS/HVP/HUGO Sequence Variant Description Working Group (SVD-WG), addressed to "Varnomen @ variome.org", Subject: SVD-WG003. Comments need to be sent ultimately July 16, 2015).

Exon del/dup descriptions

Deletions (duplications) detected by MLPA tests (testing all exons) should be described using the format c.(649+1_650-1)_(1331+1_1332-1)del.

NOTE:  the format suggested originally to describe deletions/duplications detected by MLPA tests (testing all exons) is like c.650-?_1331+?del, i.e. a deletion starting in the intron preceding c.650 (first nucleotide of the first deleted exon) and ending in the intron after c.1331 (last nucleotide of the last deleted exon). This format conflicts with the basic format to describe deletions/duplications where the break point was not sequenced but where a region of uncertainty is present (see Uncertainties). This format is (last-normal_first-changed)_(last-changed_first-normal). The Committee considered the format c.(649_650)_(1331_1332)del which is shorter but not specifically indicates that the expected break points of the change are in an intron.
NOTE:  to be 100% accurate one should not use the position of the introns in the description of the change but the location of the probes actually tested in the assay. The current proposal bears in mind that: i) it is not straightforward what probe position to use (see Uncertainties), ii) the additional detail would hardly add useful information, and iii) we should preferably not deviate too far from the original proposal (i.e. to use flanking intron locations). When one wants to use probe locations (e.g. with breakpoints in large exons) the suggestion is to use the central position of the probes in variant descriptions.

Examples;

NOTE:  the description "dup" may by definition (see Standards) only be used when the additional copy is located directly 3'-flanking the original copy (a tandem duplication). In most cases there will be no experimental proof, one simply detects the presence of an additional copy that in theory can be anywhere in the genome (inserted / transposed). Discussions are ongoing how to include this uncertainty best in the description: a proposal will follow later.


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