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Hi Kenric,<br>
<br>
Thanks for this report - you have found a bug in the way the parsing
code handles variants starting in the exon and ending in the intron.
The code is updated in branch 83 and we hope to schedule an update
to the REST server to incorporate this fix. <br>
<br>
You should see that variants lying entirely within the intron do
return the expected result, for example:<br>
<br>
wget -q --header='Content-type:application/json'
'Content-type:application/json'
'<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643+1_3643+2delGTinsAA?hgvs=1&ccds=1&canonical=1">http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643+1_3643+2delGTinsAA?hgvs=1&ccds=1&canonical=1</a>'
-O -<br>
[{"assembly_name":"GRCh38","end":136507304,"seq_region_name":"9","transcript_consequences":[{"gene_id":"ENSG00000148400","distance":2458,"variant_allele":"AA","biotype":"processed_transcript","gene_symbol_source":"HGNC","consequence_terms":["upstream_gene_variant"],"strand":-1,"hgnc_id":"HGNC:7881","gene_symbol":"NOTCH1","transcript_id":"ENST00000494783","impact":"MODIFIER"},{"gene_id":"ENSG00000148400","canonical":1,"variant_allele":"AA","biotype":"protein_coding","gene_symbol_source":"HGNC","hgvsc":"ENST00000277541.6:c.3643+1_3643+2delGTinsAA","consequence_terms":["splice_donor_variant"],"ccds":"CCDS43905.1","strand":-1,"hgnc_id":"HGNC:7881","gene_symbol":"NOTCH1","transcript_id":"ENST00000277541","impact":"HIGH"}],"strand":-1,"id":"ENST00000277541.6:c.3643+1_3643+2delGTinsAA","allele_string":"GT/AA","most_severe_consequence":"splice_donor_variant","start":136507303}]<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 18/01/2016 11:38, Kenric Leung
wrote:<br>
</div>
<blockquote
cite="mid:0C0A3D48-1280-4462-B8B4-CC4566FE8705@sanger.ac.uk"
type="cite">
<pre wrap="">Hi,
I’m trying to submit some hgvs annotations via the REST service and it looks like the endpoint has some problems dealing with +/- symbols.
Example:
wget -q --header='Content-type:application/json' '<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/vep/human/hgvs/9:g.136507304_136507305delCCinsAA?hgvs=1&ccds=1&canonical=1">http://rest.ensembl.org/vep/human/hgvs/9:g.136507304_136507305delCCinsAA?hgvs=1&ccds=1&canonical=1</a>' -O -
which gives me back an hgvs result ENST00000277541.6:c.3643_3643+1delGGinsTT
Now if I use this syntax and go to the same endpoint:
wget -q --header='Content-type:application/json' <a class="moz-txt-link-rfc2396E" href="http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643_3643+1delGGinsTT?hgvs=1&ccds=1&canonical=1">"http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643_3643+1delGGinsTT?hgvs=1&ccds=1&canonical=1"</a> -O -
I get 400 response code.
I’ve tried replacing the + symbol with %2B and that doesn’t seem to work either.
Is there any way I can use the REST service with hgvs that has intronic regions?
Thanks,
Kenric</pre>
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</pre>
</blockquote>
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