[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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