Find matching rs number for a list of gene/HGVS/cDNA data

Question

[fleurg]

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

Answer 1

[genecats.ucsc]

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 [e-mail], that way our entire team will see the question and can help with a solution.

Thanks,

ChrisL from the UCSC Genome Browser