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Hi,<br>
<br>
we encountered one variant that gives a bit confusing annotation
output from VEP (GRCh37, release 82).<br>
<br>
The variant is: 19:41133005 G>A (rs200607327).<br>
<br>
If it's still available, an online VEP annotation can be found here:
<a class="moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=1Vp8p7UidQSVCQfB-1297423">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=1Vp8p7UidQSVCQfB-1297423</a>
.<br>
<br>
<br>
We use Refseq transcript output for <span style="color:black">NM_003573.2,</span>
and got the following:<br>
<br>
<span style="color:black">NM_003573.2:c.4200G>A |</span><span
style="color:black"> NP_003564.2:p.Met1400Ile | ATG/ATA<br>
<br>
For the corresponding Ensembl transcript </span><span
style="color:black"><span style="color:black">ENST00000204005 </span>[1],
we get the following:<br>
<br>
ENST00000204005.9:c.4198G>A | ENSP00000204005.9:p.Gly1400Arg |
GGG/AGG<br>
<br>
In dbSNP and other databases, the correct cDNA position for the
RefSeq transcript for this variant is 4201, not 4200.<br>
<br>
So I have two questions:<br>
<br>
1. Why is there a three base difference between the two
transcripts (4201 vs 4198)?<br>
<br>
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.<br>
<br>
<br>
Best regards,<br>
Svein Tore Koksrud Seljebotn<br>
<br>
<br>
[1]
<a class="moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000090006;r=19:41099072-41135725;t=ENST00000204005;tl=1Vp8p7UidQSVCQfB-1297423">http://grch37.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000090006;r=19:41099072-41135725;t=ENST00000204005;tl=1Vp8p7UidQSVCQfB-1297423</a><br>
</span>
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