Obtain intron c. offset using REST API

[rickymagner]

Hi, I was using the VEP REST API to annotate some variants, and I was wondering if it was possible to return the intron c. offset for an intronic variant? For example, suppose I have this variant in c. notation: ENST00000269305.9:c.560-1G>A. Then I would want to get the value -1 as the offset into the intron. Or e.g. ENST00000269305.9:c.560-39G>T should have offset -39.

I know I can do some string parsing on the HGVSc returned, but was wondering if this was already available given we can get back e.g. CDNA position, CDS position, and protein position from the API.

[dglemos]

Hi @rickymagner,
At the moment it's not possible to get the hgvs offset from the API. I'll talk to the team to determine if this is something we can do.

Best wishes,
Diana

[rickymagner]

Thanks. In a similar vein, it may also be useful to get the cdna_start/end for deletions that begin/end in introns (e.g. for something like c.563-3_578+8del still have cdna_start = 563 etc. as you can tell where it "actually" is by coming this with the intron offset. This would be useful for e.g.checking overlap with a feature expressed in c. coordinates already.