Proposal SVD-WG009 (conversion)
- Status: open
- proposal SVD-WG009 opened for Community Consultation on August 1 (2020) and will be closed October 31 (2020).
The proposal suggests simplification of the HGVS nomenclature by discontinuing the use of the variant type “con” to describe conversions (see Conversion). Comments to the proposal, positive or negative, should be addressed to “Varnomen @ variome.org” (remove the spaces), Subject: SVD-WG009.
According to the HGVS definitiona conversion is a sequence change where, compared to a reference sequence, a range of nucleotides are replaced by a sequence from elsewhere in the genome.
- the HGVS recommendations do not need the “con” format since such variants can be described using the existing “delins” format (simply replace “con” by “delins” in the description).
- the format is rarely used, so the change should not cause significant problems
- stopping the use will help to simplify the HGVS recommendations
- previously NC_000022.10:g.42522624_42522669con42536337_42536382, a conversion in exon 9 of the CYP2D6 gene on cromosome 22 (NC_000022.10) replacing exon 9 nucleotides g.42522624 to g.42522669 with nucleotides g.42536337 to g.42536382 of the 3’ flanking CYP2D7P1 gene
- previously NC_000012.12:g.6128479_6128749con[NC_000022.11:g.17178616_17178886], a gene conversion in the VWF gene converting the chromosome 12 sequence (NC_000012.12) from position g.6128479 to g.6128749 with the sequence from chromosome 22 (NC_000022.11) from position g.17178616 to g.17178886.
- NOTE: for inserted sequences derived from another reference sequence the prefix of the reference sequence type (“g.” in the example) needs to be provided.