[ensembl-dev] null type of consequence

Sung Gong sung at bio.cc
Thu Oct 13 14:17:49 BST 2011


Hi Graham,

Thanks for fixing the bug and updating CVS.
Just to let you know that my script works fine after updating local
Ensembl-variation API (cvs -q update -d -P -r branch-ensembl-64).

Cheers,
Sung

On 10 October 2011 16:03, Graham Ritchie <grsr at ebi.ac.uk> wrote:
> Hi Sung,
>
> It should not be possible to have a 'null' consequence for a variant, but there is currently a slight bug with the API code used by the VEP with variants that fall in short artificial introns, such as your example below. If you look on the exon sequence view of this transcript here:
>
> http://www.ensembl.org/Homo_sapiens/Transcript/Exons?g=ENSG00000178295;r=2:17953948-17963491;t=ENST00000536097
>
> You can see that the final intron of the transcript is only 5 bps long, and your variant falls on the first base of this intron. We don't want to call such variants intronic or any of the splicing consequences as these very short introns are generally not real, but they should get some consequence term assigned. We will fix this for the next release.
>
> Sorry for any confusion caused.
>
> Cheers,
>
> Graham
>
>
> On 10 Oct 2011, at 15:46, Sung Gong wrote:
>
>> Hi,
>>
>> Is it possible to have a 'null' (or empty) consequence type for a given variant?
>>
>> I thought something went wrong with my script, so double check with
>> the VEP web version.
>> However the VEP also shows a null value as a consequence type for my
>> variant as shown at the 2nd line below:
>>
>> Uploaded Variation    Location        Allele  Gene    Feature Feature
>> type  Consequence     Position in cDNA        Position in CDS Position in
>> protein       Amino acid change       Codon change    Co-located Variation    Extra
>> 2_17962994_A/G        2:17962994      G       ENSG00000178295 ENST00000536097 Transcript              -       -       -       -       -       rs113873109,rs79148917  HGVSc=ENST00000536097.1:c.1425+1A>G
>> 2_17962994_A/G        2:17962994      G       ENSG00000163029 ENST00000428868 Transcript      INTRONIC        -       -       -       -       -       rs113873109,rs79148917  HGVSc=ENST00000428868.1:c.-6+6088T>C
>> 2_17962994_A/G        2:17962994      G       -       ENSR00000585885 RegulatoryFeature       REGULATORY_REGION       -       -       -       -       -       rs113873109,rs79148917  -
>> 2_17962994_A/G        2:17962994      G       ENSG00000178295 ENST00000528873 Transcript      DOWNSTREAM      -       -       -       -       -       rs113873109,rs79148917  -
>> 2_17962994_A/G        2:17962994      G       ENSG00000178295 ENST00000317402 Transcript      NON_SYNONYMOUS_CODING   2640    2515    839     K/E     Aag/Gag rs113873109,rs79148917  PolyPhen=possibly_damaging(0.556);HGVSc=ENST00000317402.7:c.2515A>G;HGVSp=ENSP00000318977.7:p.Lys839Glu;Condel=deleterious(0.634);SIFT=deleterious(0)
>> 2_17962994_A/G        2:17962994      G       ENSG00000178295 ENST00000381254 Transcript      NON_SYNONYMOUS_CODING   2729    2515    839     K/E     Aag/Gag rs113873109,rs79148917  PolyPhen=possibly_damaging(0.556);HGVSc=ENST00000381254.2:c.2515A>G;HGVSp=ENSP00000370653.2:p.Lys839Glu;Condel=deleterious(0.634);SIFT=deleterious(0)
>> 2_17962994_A/G        2:17962994      G       ENSG00000163029 ENST00000402989 Transcript      INTRONIC        -       -       -       -       -       rs113873109,rs79148917  HGVSc=ENST00000402989.1:c.-6+6088T>C
>>
>> How can I interpret this?
>>
>> Cheers,
>> Sung
>>
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>
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