[ensembl-dev] new VEP REST endpoint

Will McLaren wm2 at ebi.ac.uk
Thu Dec 11 09:07:42 GMT 2014

Hi Michael,

You should no longer see the somatic status under the
transcript_consequences objects; this was a bug and should only appear in
the colocated_variants objects. I think if you check the output again you
should see this has already been fixed.

You can always get the reference allele from the allele_string field at the
root of the JSON object; this is a "/"-separated string where the first
allele is the reference allele.

The allele given in allele_string and in the variant_allele field are
always the alleles as input; typically this will be on the forward strand.
This allows you to easily identify which of the alleles from allele_string
the variant_allele refers to, particularly useful in the case of input
variants with multiple alternate alleles.

The HGVS representation is relative to the transcript that it overlaps, so
if the transcript is on the reverse strand the alleles get
reverse complemented, hence why A->T becomes T->A in the HGVS string
for ENST00000479537
(a reverse strand transcript, as indicated by "strand: -1"). You can see
this also in the codons field.

This is maybe clearer if you look at a variant where the ref/alt alleles
are not the complement of each other, e.g.

The incorrect SO terms have been updated a while ago; those GEMINI
documents refer to a non-current version of VEP.


Will McLaren
Ensembl Variation

On 10 December 2014 at 21:55, Michael Heuer <heuermh at gmail.com> wrote:

> On Wed, Dec 10, 2014 at 12:05 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> Hello,
>> I'm finally getting the chance to update some code that depends on the
>> VEP REST endpoint from the beta version to the current production version
>> and have a few questions.  Looking specifically at this example
>> http://rest.ensembl.org/vep/human/id/COSM476?content-type=application/json
>> Under transcript_consequences in this example somatic is "1,1,1".  What
>> is this supposed to represent?  There are three colocated_variants, so I
>> assume this is referring to that.
>> Under transcript_consequences allele_string="A/T" is now represented as
>> variant_allele="T".  It would be useful to have a similar
>> reference_allele="A".
> I'm sorry, I might have this backward; COSMIC defines this variation as
> Mutation Id: COSM476 AA Mutation: p.V600E ( Substitution - Missense ) CDS
> Mutation: c.1799T>A ( Substitution )
> http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=476
> codons/amino_acids and HGVS appear correct but allele_string and
> variant_allele have it flipped, shouldn't allele_string be "T/A",
> variant_allele "A" and reference_allele "T"?
>    "id": "COSM476",
>    "allele_string": "A/T",
>    "transcript_consequences": [
>       {
>         "variant_allele": "T",
>         "codons": "gTg/gAg",
>         "hgvsc": "ENST00000479537.3:c.83T>A",
>         "amino_acids": "V/E",
>         "hgvsp": "ENSP00000418033.1:p.Val28Glu",
>   }
>    michael
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