Covert cDNA or gDNA position to protein position

Question

[andrewreview3]

Hello,

I have a frameshift mutations described at the cDNA and genomic DNA levels. It is a small deletion of four nucleotides. I'd like to see its HGVS nomeclature at the protein level, like in the following example: p.(Arg97Profs*23).

Does anyone know a free online software to do that just for a single mutation? I don't need to do it for several mutations in a vcf. Just one mutation.

Thanks,

Andy

Answer 1

[Denise CS]

Use the Ensembl Variant Effect Predictor aka the VEP. Besides getting further annotation for that variant in HGVS identifiers you will find out its genomic coordinates and also cDNA and if it's known in other databases such as dbSNP. You can run VEP in a web interface, as a Perl script or using the Ensembl REST API.