How to retrieve gene annotation "HGVS cDNA" (e.g. c.158G>A) by chromosome position

Question

[merobin8]

How can I convert chromosome position (e.g GRCh37/hg19 position,12:103306579 C/T) to HGVS cDNA (e.g c.158G>A) ? Currently I have got the file refGene.txt , and hg19.fasta , I can retrieve relative info like Alleles (ref/alt) , Transcript, sequence etc. But when try to calculate the position of HGVS cDNA which is 158 , I find my result doesn't match . Can anyone tell me how to caculate the postion in HGVS cDNA ?

Answer 1

[cpad0112]

http://grch37.rest.ensembl.org/vep/human/hgvs/12:g.103306579C>T?content-type=application/json;hgvs=1

using Ensembl grch 37 rest api and final format is in json format. Filter by hgvsc (ENST00000553106.1:c.158G>A)

If you parse the json for hgvsc and hgvsp, you would some thing like this:

ENST00000307000.2:c.143G>A  ENSP00000303500.2:p.Arg48His
ENST00000546844.1:c.158G>A  ENSP00000446658.1:p.Arg53His
ENST00000548677.1:n.245G>A  
ENST00000548928.1:n.80G>A   
ENST00000549111.1:n.254G>A  
ENST00000550978.1:n.142G>A  
ENST00000551337.1:c.158G>A  ENSP00000447620.1:p.Arg53His
ENST00000551988.1:n.247G>A  
ENST00000553106.1:c.158G>A  ENSP00000448059.1:p.Arg53His

[merobin8]

Thank you for your suggestion. This will save me a lot of effort , but is it possible to make it localized ? I mean we won't have to rely on the interfaces provided by the third party and produce the result by our own, since it may not be available in the future .

[cpad0112]

one of the easy to use and offline setup tools is transvar (IMO). If you want offline HGVS translation, you need to download and set up appropriate genome files and annotation files.

[Emily]

Yes, you can install a local cache of the VEP data and run it from the command line.