VEP classifies exonic variants as downstream

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10 months ago

tvrlisml ▴ 20

Hello,

I am using VEP to annotate my variants. As defined in the web page of Ensembl, upstream and downstream variants located at 5' and 3' regions of genes however, in variant consequences I see that variants which are categorized as upstream or downstream variants by VEP are located at exonic/genic regions. As an example, variant seen in the picture is categorized as an upstream gene variant however it is located at an exonic region. For this issue I tried setting --distance parameter to 500 bp. However, I still see upstream and downstream variants at genic locations. Why is that happening?

Variant categorized as an upstream gene variant by VEP

ensembl vep • 643 views

ADD COMMENT • link updated 10 months ago by colindaven 7.0k • written 10 months ago by tvrlisml ▴ 20

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check the VEP build, check your both using the same source of genes.

ADD REPLY • link 10 months ago by Pierre Lindenbaum 164k

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I noticed the same thing and was wondering why But I couldn't understand what you said, unfortunately, can you explain a little more?

ADD REPLY • link 10 months ago by Meryem • 0

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There are many sources of gene annotation. Which did you use with VEP ? Maybe one from Ensembl itself ? This site is near Cambridge in the UK.

It looks from the browser screenshot that you are checking against NCBI RefSeq. This is data from the USA NCBI. So not Ensembl. There are other annotation sources, notably Gencode and UCSF.

Please check all these via google and read up on it, maybe comparative review articles also exist ?

ADD REPLY • link 10 months ago by colindaven 7.0k

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