Question: Find matching rs number for a list of gene/HGVS/cDNA data
1
gravatar for fleurg
5 months ago by
fleurg10
fleurg10 wrote:

HI! I would like to get an rs number using (any) of the following information that I have in a data spreadsheet Gene name (e.g. EXOSC3)/ HGVS cDNA (old nomenclature) (e.g. c.92G>C)/ HGVS protein (p.G31A for protein)/ cDNA_reference (e.g. NM_016042.2) I was thinking that this would be relatively straightforward - i.e. download similar data with rs number - then merge the files - but can't find this! Would be extremely grateful if anyone can help, Thanks so much, Fleur

snp gene • 223 views
ADD COMMENTlink modified 5 months ago by genecats.ucsc340 • written 5 months ago by fleurg10
3
gravatar for genecats.ucsc
5 months ago by
genecats.ucsc340
genecats.ucsc340 wrote:

You can use the UCSC Genome Browser to get this information, but the process depends on the specific HGVS terms you have.

The general idea is to split your list into two lists, one with just your different HGVS terms, and one with just your gene names. Then you can use a combination of the Table Browser and Data Integrator to get the rsID's (if any) corresponding to your gene names, and the Variant Annotation Integrator to get the rsID's (if any) corresponding to your HGVS terms.

We can provide more specific steps if you email this question along with some example data to our mailing list genome@soe.ucsc.edu, that way our entire team will see the question and can help with a solution.

Thanks,

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 5 months ago by genecats.ucsc340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 537 users visited in the last hour