[ensembl-dev] hgvs intronic syntax using VEP rest service

[Sarah Hunt]

Hi Kenric,

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.

You should see that variants lying entirely within the intron do return 
the expected result, for example:

wget -q --header='Content-type:application/json' 
'Content-type:application/json' 
'http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643+1_3643+2delGTinsAA?hgvs=1&ccds=1&canonical=1' 
-O -
[{"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}]

Best wishes,

Sarah

On 18/01/2016 11:38, Kenric Leung wrote:
> 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' 'http://rest.ensembl.org/vep/human/hgvs/9:g.136507304_136507305delCCinsAA?hgvs=1&ccds=1&canonical=1' -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' "http://rest.ensembl.org/vep/human/hgvs/ENST00000277541.6:c.3643_3643+1delGGinsTT?hgvs=1&ccds=1&canonical=1" -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
>
>
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