SVD WG009

Community Consultation#

Proposal SVD-WG009 (conversion)#

Status: accepted

proposal SVD-WG009 opened for Community Consultation on August 1, 2020, closing on October 31, 2020. Since no major objections were received, the SVD-WG decided to accept the proposal.

Based on the proposal, the HGVS nomenclature pages have been updated (November 2020); the specific conversion pages were removed and 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.

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#

  • 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 chromosome 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.

  • 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.