Extracting the near amino acid number from an essential splice site variant

Question

[jafisep314]

Hi all,

I have some essential splice site variants, and I am trying to find a systematic way to derive the nearest amino acid number to the variants. For example, I have 1:6522052:A:G (GRCh37), and it's HGVS is TNFRSF25(NM_003790.3):c.925+2T>C. Using the UCSC Genome Browser, it seems that the closest amino acid sequence to it is L125.

Does any of you know a way to be able to systematically do this for a larger number of variants? I really appreciate any input at all, thank you very much!

Answer 1

[Ram]

The python HGVS module has a way to go from genomic change to transcript change to protein change. See: https://hgvs.readthedocs.io/en/stable/examples/using-hgvs.html#projecting-variants-between-sequences and the more functional https://github.com/biocommons/hgvs/blob/main/examples/using-hgvs.ipynb

EDIT: However, your example is a splice site variant so mapping to a "nearby" amino acid might mean knocking off the +2 part manually then mapping to the p. coordinate.