HGVS annotations now available on PharmVar

We are excited to share that PharmVar is now providing HGVS annotations in addition to their more traditional annotations. To accommodate different styles, the Variation Window has been redesigned.

Clicking on any SNV on a PharmVar gene page will activate the variation window. The example shown below is for the CYP2C9*2 variant c.430C>T. This view provides SNV positions across all sequences, the link to the NCBI dbSNP identifier (rs number) as well as SNV frequency. There is also a bar providing the option to display all haplotypes with the selected variant.

The top portion of the variation window displays SNV coordinates according to Human Gene Variation Society (HGVS) nomenclature on the gene, transcript and genome (GRCh37 and GRCh38) levels. Coordinates are displayed as obtained through the NCBI Variation Services. 

The middle portion of the variation window displays SNV positions ‘PharmVar-style’ on the gene, transcript and genome (GRCh37 and GRCh38) levels giving positions for both count modes and detailing the reference and variant nucleotides. 

It is noted that HGVS and ‘PharmVar-style’ positions may differ for insertion/deletion variants in some instances, which is most likely explained by how sequences are aligned. Also, PharmVar displays single nucleotide insertions as ‘ins’ while HGVS displays them as duplications or ‘dup’. Additional details and examples are can be found in the PharmVar ‘Standards’ document. HGVS annotations are also accessible via API services.

PharmVar welcomes any feedback you may have through support@pharmvar.edu.