[ensembl-dev] Fwd: problem with some mutations, like TP53:c.110_120delinsC

[Oliver Langenhorn]

Hi,

I am trying to annotate a list of mutations in coding HGVS notation with
VEP, most of them go through pretty ok, but some are creating troubles. One
example is TP53:c.110_120delinsC, here's the job output:
https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=fbegKEYtZPdXtACp-9377859

And that's the relevant part from the VCF:
17 7676249 TP53:c.110_120delinsC CCATTGCTTGG C . .

Whenever i try to use the generated VCF downstream, there are issues
because sequence starting at 17:7676249 in GRCh38 isn't actually *C*CATTGCTTGG
like in VEP-generated VCF. It is shorter: CATTGCTTGG, see that here:
https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7676249-7676259

And so there's a reference mismatch. I am missing something obvious?

Cheers,
Oliver
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20230726/e9c16073/attachment.html>