[ensembl-dev] VEP - HGVS duplication reported as insertion

[Daniel Borras]

Dear Sir, Madame, 

My name is Daniel Borras and I am currently working with your tool Variant Effect Predictor. I usually input HGVS variants obtained from other sources to annotate their effect. However I noticed an unexpected behaviour when it comes to duplications. When feeding VEP with an HGVS duplication this is transformed to an insertion, please the real output below. According to HGVS recommendations, duplications are reported differently than insertions, let me quote HGVS recommendations: g.5dupT (or g.5dup, not g.5_6insT ) . This wouldn't be a big issue if it wasn't because for downstream analysis the annotation of the variant changes making previous comparisons and checks to fail since the variant description is different. I believe that this behaviour should be patched, probably is not too complicated to fix, and will make VEP to report correct duplications in HGVS notation. 

The results are I obtained are: 
Input: NM_001009944.2:c.4248dup 
Output: NM_001009944.2:c.4248_4249insT 
Row: chr16 2160919 NM_001009944.2:c.4248dup C CA . . A|frameshift_variant|HIGH|PKD1|5310|Transcript|NM_001009944.2|protein_coding|15/46|| NM_001009944.2:c.4248_4249insT |NP_001009944.2:p.Gly1417TrpfsTer14|4457-4458|4248-4249|1416-1417|-/X|-/T|||-1|insertion|||YES|||NP_001009944.2||||rseq_mrna_nonmatch&rseq_cds_mismatch&rseq_ens_match_wt||||||||||||||||||||| 

The results were obtained by using: 
VEP version: ensembl-tools-release-80 
Assembly: GRCh37 
Cache_version: 80 
Port: 3337 


Best, 
Dani 


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160108/bdc53edc/attachment.html>