Convert HGVS formatted transcript aligned RNA notated mutations to chr:pos coordinates

Question

[msnyder424]

I have a small number of RNA mutations in HGVS format and I want to convert them into chr:pos coordinates. These mutation are mostly fusions but some SNPs. They are all in RNA notation with a transcript supplied.

Below are some examples of some of the HGVS formatted mutations I am trying to convert. For the fusions (the first two), I only need the "breakpoints" in bold.

Gene HGVS
CCDC6-RET NM_005436.5:r.1_435::NM_020975.6:r.2327_5617
CD74-ROS1 NM_001025159.2:r.1_812::NM_002944.2:r.5757_7368
EGFR Variant NM_005228.5:r.350_1150del

I prefer to do everything programmatically, but I have <50 of these so a brute force method would work, too.

Thanks!

[Ram]

The python hgvs module might help.