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!
•
written
by
jafisep314 •
1 answer
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.
Log in to answer this question.
-
Strugling on the 3'rule of HGVS
written by lacb •
-
Inconsistency between VCF and HGVS
written by Senanu •
-
Struggling with protein context of Annovar output
written by papp.benjamin.t •
-
Mapping GeneSymbol plus cDNA position to a Chr:Position ... without transcript ID.
written by LauferVA
-
How to convert amino acid sequence to numbers
written by nrizzolo1796 •
-
Inquiry related to vcf file and formatting
written by rheab1230 •
-
Identifying protein impact
written by ira •
-
Synonymous variants annotated using Variant studio not having HGVS p. amino acid names
written by amk •
-
Next-generation DNA sequencing: How to tell systematic errors from real SNVs?
written by robles.daniela
-
Vep Not Giving Annotation With Refseq Transcript
written by Vivek
