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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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HGVS notation for dup in 109 becomes ins in 110 #1633

Open barbarian1803 opened 3 months ago

barbarian1803 commented 3 months ago

Describe the issue

For below variant:

#CHROM POS ID REF ALT QUAL FILTER INFO chr21 5233678 . A AATTT . . .

In VEP 109.3, this variant has HGVS notation: ENST00000623753.1:n.132-758_132-755dup In VEP 110.1/111.0, this variant has notation: ENST00000623753.1:n.132-755_132-754insAAAT I notice a lot of similar variant that used to be dup becomes ins in VEP 110 and 111. The correct notation would be the dup.

Another example

#CHROM POS ID REF ALT QUAL FILTER INFO chr21 13933439 . C CT . . . It used to be : ENST00000451663.5:n.2429+398dup now becomes: ENST00000451663.5:n.2429+398_2429+399insA

Additional information

Run via docker for version 110.1 and VEP web for latest version v111.

System

likhitha-surapaneni commented 3 months ago

Hi @barbarian1803 , Thank you for reporting to us. There is a fix applied in the upcoming release to address the issue. With this, the HGVSc would be reported as dup instead of ins.

Kind regards, Likhitha

GSYongWu commented 3 months ago

I have encountered the same problem and hope it can be updated as soon as possible.

aksenia commented 2 weeks ago

Hi is this still an issue in v112? thank you!

GSYongWu commented 2 weeks ago

This issue is resolved, but I have discovered a new problem. The CDS coordinates for some genes are incorrect. For example, the mutation SRGAP2:NM_015326.5, c.85A>T(p.T29S) has been annotated as c.994A>T(p.T332S). I suspect it is a database issue.