Reece Hart
Reece Hart
hgvs 1.2.3 gives: ```python >>> var_c = hp.parse_hgvs_variant('NM_004119.2:c.1756_1757insGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAATTTAGAGTTTGAG') >>> var_p = vm.c_to_p(var_c) >>> str(var_p) 'NP_004110.2:p.(Ser585_Asp586insGlyAspArgLeuLeuArgTerTerValLeuLeuArgTerPheGlnArgIleTerIleTerSerGlnMetGlyValSerLysArgLysPheArgValTer)' ``` I suspect that the difference is due to recent fixes (#474, #492). ~~From the...
You're right, @AngieHinrichs. Coming back to the original example, I don't see any guidance for whether this should be written as `p.Ser585_Asp586ins…` or `p.Asp586delins`. Both seem plausible to me on...
I believe that the 585_586delins version is preferable. This trivial case may shed light on the issue: Imagine a SNV that converts Asp at 586 to Ter. Clearly, that should...
This question was raised on the HGVS Facebook page (sigh). Facebook is a closed system (you have to have an account to view the page). Here's the text: > Q:...
Yes, we should implement what HGVS recommends here. That is, we should revert to the original behavior, but add Ter. In rereading this thread, I realized that I was so...
IVS syntax is not part of HGVS recommendations. So, the only use case for IVS is to translate old variants into base-offset positions (e.g., c.123-4). I don't think we'd ever...
IVS (and EX) variants imply an exon structure, but most such variants don't specify a transcript. Therefore, such variants are roughly like street addresses without the street name. The reason...
I'm game for brainstorming! I'd like to solve this, but only if it's reliable. I already have a script to kinda do what you suggested in [hgvs-guess-plausible-transcripts]( https://github.com/biocommons/hgvs/blob/master/misc/experimental/hgvs-guess-plausible-transcripts). It works...