[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
More information about the Dev
mailing list