How to write HGVS nomination for noncoding intergenic variants

Question

[hsamireh]

I want to generate HGVS nomination for each variant I have on a file. For the coding ones it is easy and I also know how to generate for noncoding intron/exon variants. However, I have no clue on how to do so for non-coding intergenic ones. For example I have a variant chr1:g.29894C>A which is noncoding and occurs upstream region of gene OR4GP. how would I generate an hgvs nomination for this variant?

[cpad0112]

use ensembl API: https://rest.ensembl.org/documentation/info/vep_hgvs_get and https://rest.ensembl.org/documentation/info/vep_hgvs_post

https://rest.ensembl.org/vep/human/hgvs/chr1:g.29894C%3EA?content-type=application/json

Answer 1

[manuel.belmadani]

There's some documentation on: https://varnomen.hgvs.org/, specifically see here under non-coding variants: https://varnomen.hgvs.org/bg-material/refseq/ (see also: https://varnomen.hgvs.org/bg-material/consultation/svd-wg002/)

Personally I usually handle it through some tool. You can do the conversion from genomic, cDNA, Protein coordinates to any other in batch using Transvar ( available on the web or as a command-line tool.) https://bioinformatics.mdanderson.org/transvar/

Interestingly transvar doesn't use the n. prefix for lincRNAs. I might not be exactly standard. chr1:g.29894C>A ENST00000473358 (lincRNA) MIR1302-10 + chr1:g.29894C>A/c.341C>A/. inside_[noncoding_exon_1] CSQN=UnclassifiedSNV;source=Ensembl

I tried with something else that's not a lincRNA and I get this:

10:g.2019099T>A .   .   .   
chr10:g.2019099T>A/./. 
inside_[intergenic_between_LINC00700(4,751_bp_upstream)_and_LOC105376347(52,699_bp_upstream)]   
CSQN=IntergenicSNV

So here it doesn't even give me a cDNA variant. Seems like following the HGVS specification is the safest bet, though I'm not sure if Transvar correctly interprets the lincRNAs.