[ensembl-dev] VEP GRCh37 REST returns incorrect start position for deletion?

ls lshen86 at gmail.com
Fri Feb 13 14:00:46 GMT 2015


The VEP returned start position is same as stop position, which is 
suspicious for me.

http://grch37.rest.ensembl.org/vep/human/hgvs/1:g.19377071_19377074del?content-type=application/json


[{"assembly_name":"GRCh37","end":19377074,"seq_region_name":"1","strand":1,"id":"1:g.19377071_19377074del","intergenic_consequences":[{"consequence_terms":["intergenic_variant"]}],"allele_string":"CCCG/-","most_severe_consequence":"intergenic_variant","start":19377074}]


OR with delCCCG in input:
http://grch37.rest.ensembl.org/vep/human/hgvs/1:g.19377071_19377074delCCCG?content-type=application/json

[{"assembly_name":"GRCh37","end":19377074,"seq_region_name":"1","strand":1,"id":"1:g.19377071_19377074delCCCG","intergenic_consequences":[{"consequence_terms":["intergenic_variant"]}],"allele_string":"CCCG/-","most_severe_consequence":"intergenic_variant","start":19377074}]




# my reformatted text:

Input:  1:g.19377071_19377074del

VEP output:

Assembly_name : GRCh37
Chromosome : 1
Start : 19377074
End : 19377074
ID : 1:g.19377071_19377074del
Allele_string : CCCG/-
Most_severe_consequence : intergenic_variant
HGVS_g: 1:g.19377074delCCCG




Lishuang Shen





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