Proposal SVD-WG009 (conversion)
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- Status: accepted
- proposal SVD-WG009 opened for Community Consultation on August 1 (2020), closed October 31 (2020).
Based on the proposal the HGVS nomenclature pages have been updated (November 2020); the specific conversion pages were removed, information was merged with the Deletion-Insertion pages.
The proposal suggested to simplify the HGVS nomenclature by discontinuing the use of the variant type “con” to describe conversions (see Conversion).
According to the HGVS definition a 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
Examples
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- NC_000022.10:g.42522624_42522669delins42536337_42536382
- 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
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- NC_000012.12:g.6128479_6128749delins[NC_000022.11:g.17178616_17178886]
- 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.