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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Annotation confusion #280

Open cheanney opened 4 months ago

cheanney commented 4 months ago

Hi,

First of all, we want to thank you for this wonderful application. It has streamlined our variant annotation workflow tremendously.

We submitted the HG19 chr16-11349332-CC-TT variant to OpenCravat and received the following results:

cDNA change: c.3_4delinsAA Protein change: p.Val2_Met119del As you can see, the cDNA change does not match the protein change p.Val2_Met119del. Not sure why this variant which is in the initiator methionine is being called a large deletion Val2_Met119del. It is only a 2-nucleotide deletion.

Screenshot 2024-07-30 at 10 55 52 AM

Then, we submitted this variant to VEP and VarSome, and the results were:

cDNA change: c.3_4delGGinsAA Protein change: p.(Met1_Val2delinsIleIle) VarSome Result

Screenshot 2024-07-30 at 12 35 43 PM

Here are the cDNA and protein locations from vep:

Screenshot 2024-07-30 at 12 38 20 PM

Let me know if we can provide additional information.

Best,

Anney

jasminebro commented 4 months ago

Hi, we will take a look at this issue! Thank you for the information.