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

[Diana Lemos]

Hi Oliver,

Thanks for reporting this issue.

We are looking into it - I'll let you know when we know more.


Best wishes,

Diana



On 26/07/2023 13:27, Oliver Langenhorn wrote:
> 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
>
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