[ensembl-dev] Strange Ensembl/RefSeq VEP annotation for variant

Svein Tore Koksrud Seljebotn s.t.seljebotn at medisin.uio.no
Wed Dec 2 11:55:45 GMT 2015


Hi,

we encountered one variant that gives a bit confusing annotation output 
from VEP (GRCh37, release 82).

The variant is: 19:41133005 G>A (rs200607327).

If it's still available, an online VEP annotation can be found here: 
http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=1Vp8p7UidQSVCQfB-1297423 
.


We use Refseq transcript output for NM_003573.2, and got the following:

NM_003573.2:c.4200G>A |NP_003564.2:p.Met1400Ile | ATG/ATA

For the corresponding Ensembl transcript ENST00000204005 [1], we get the 
following:

ENST00000204005.9:c.4198G>A | ENSP00000204005.9:p.Gly1400Arg | GGG/AGG

In dbSNP and other databases, the correct cDNA position for the RefSeq 
transcript for this variant is 4201, not 4200.

So I have two questions:

1. Why is there a three base difference between the two transcripts 
(4201 vs 4198)?

2. Is there something going wrong in the calculation of the RefSeq data? 
Note the frameshift for the codons, resulting in wrong protein as well.


Best regards,
Svein Tore Koksrud Seljebotn


[1] 
http://grch37.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000090006;r=19:41099072-41135725;t=ENST00000204005;tl=1Vp8p7UidQSVCQfB-1297423
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