[ensembl-dev] null type of consequence

Sung Gong sung at bio.cc
Mon Oct 10 15:46:06 BST 2011


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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