[ensembl-dev] null type of consequence

[Graham Ritchie]

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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