Annotation confusion

[cheanney]

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.

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

Here are the cDNA and protein locations from vep:

Let me know if we can provide additional information.

Best,

Anney

[jasminebro]

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