Obtaining genomic coordinates from HGVS name

[Heitner, Steven G.]

Greetings, Legitimate Question Fans.

I noticed that the Browser now offers HGVS support.  Is the HGVS information stored in a table in SQL somewhere?

Let me describe what I’m attempting to do.  I have a data file containing several thousand variants and it includes the HGVS names (e.g., NM_144670.4:c.174_175dupCA), but no coordinate information.  I am writing a Perl script to extract the data from the file and insert it into a SQL table and I would like to also include the appropriate coordinate info.  If possible, I would like to query the UCSC tables using the HGVS names in my file to obtain that coordinate info.

If this is possible, please let me know the relevant SQL table(s) where the data is located.  I looked at the refGene and connected table schema, but I didn’t see it.  I may have just not been looking hard enough.  :)

Thanks!

Best regards,
Steve

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[Christopher Lee]

Hi Steve,

Thank you for your question about querying MySQL for HGVS information.

Unfortunately there is no table containing HGVS terms for you to query directly. However, there are a number of external tools you can use to accomplish this task:
https://github.com/zwdzwd/transvar
https://www.mutalyzer.nl/
https://bitbucket.org/biocommons/hgvs

There are also multiple threads on BioStars that will probably be of help:
https://www.biostars.org/p/15992/
https://www.biostars.org/p/6686/
https://www.biostars.org/p/6945/

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Heitner, Steven G.]

Thank you, Christopher.

I ended up using Mutalyzer.  For anyone else who may be interested in doing the same thing at some point, I used their Web Services (https://mutalyzer.nl/webservices).  The “HTTP/RPC+JSON web service” section explains how to construct a URL to retrieve data.  They have a list and description of methods at https://mutalyzer.nl/soap-api for use in constructing your URL.  In Perl, you can just assign a variable to capture the information retrieved by the URL:

my $data = get("https://mutalyzer.nl/json/numberConversion?build=hg19&variant=NM_144670.4:c.174_175dupCA");

Here, the numberConversion method will obtain the genomic HGVS notation from the coding HGVS notation.  The genomic HGVS notation includes the chromosome accession number, but you can then use the chromosomeName method to obtain the chromosome number:

my $chrom = get("https://mutalyzer.nl/json/chromosomeName?build=hg19&accNo=NC_000012.11");

I hope this is helpful for someone.  Thanks again!

--Steve