[ensembl-dev] VEP - Multiple Effects

[Cyriac Kandoth]

Hi Hans.

You'll note that splice_region_variant differs from splice acceptor/donor
variants. A splice_region_variant is anything 3-8 bps into the intron or
UTR, while the acceptor/donor annotations are given to variants within 2bp
flanks of splice junctions.

Here is a larger list of VEP consequences with descriptions, and sorted in
the order of how VEP prioritizes them:
http://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences

So in your example, the splice_region_variant and 5_prime_UTR_variant are
both valid annotations, but the first one has higher priority than the
second. In general, you can choose the first one between multiple
annotations since they seem to be ordered by priority. But I'll let one of
the Ensembl folks confirm.

~Cyriac

On Mon, Feb 9, 2015 at 6:34 PM, Hans Vasquez-Gross <
havasquezgross at ucdavis.edu> wrote:

> Hi All,
>
> How are multiple effects for a given mutation assigned?  I have a
> colleague that asked me about a VEP annotation for one of her genes of
> interest.
>
> It was classified as a splice_region_variant&5_prime_UTR_variant.  If the
> mutation was a splice_region_variant, we would be very interested in the
> sample.  But if it is a 5' UTR variant, we will be less interested in the
> mutation.  When visualizing the data, you can see this mutation occurs in
> the 5' UTR (purple) and doesn't seem to confer any splice region variant.
>
> [image: Inline image 1]
>
>
> Any insight on how multiple effects are assigned would be helpful.  I
> couldn't seem to find the info in the documentation.
>
> Thank you,
> -Hans
>
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