[ensembl-dev] No consequence for variant

Will McLaren wm2 at ebi.ac.uk
Fri Feb 5 10:44:33 GMT 2016

Hi Sebastian,

In some cases when using the RefSeq transcript cache, the mappings we are
provided by NCBI for a particular transcript may cause issues.

In this case our database contains duplicate entries for NM_001271893.1,
one of which is marked as a protein coding transcript but has no defined
CDS. Your variant overlaps this duplicate, and because of the conflicting
definition the VEP doesn't know what to call the variant and a warning is
given on STDERR and in the warnings file.

I would consider it safe to filter out or ignore any cases where we are
unable to assign a consequence type such as this as they typically
correspond to transcript annotations that are faulty to begin with.


Will McLaren
Ensembl Variation

On 3 February 2016 at 14:07, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:

> Hi Ensembl,
> I am trying to annotate a variant using VEP v83 with the
> homo_sapiens_merged cache.
> When I reach this variant in my VCF file:
> 2    239832097    .    A    T    100    PASS    .    .    .
> VEP fails with:
> Can't call method "rank" on an undefined value at
> /path/to/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1975
> The function vf_to_consequnces returns '?' as a consequence for this
> variant.
> I have taken the liberty to attach the Data::Dumper output for a couple of
> relevant variables as well as the parameters used to call the VEP script.
> When looking at the result of vf_to_consequences it seems that the Codons
> and Amino_acids fields are undefined (line 98 & 100), although the variant
> is predicted protein_coding (line 85).
> I got the same error for variants up- and downstream of that location.
> Can anyone confirm this? And if so: has an idea on how to fix it?
> Best wishes,
> Sebastian Ginzel
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