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biothings / myvariant.info

MyVariant.info: A BioThings API for human variant annotations
http://myvariant.info
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Selecting HGVS annotation of canonical transcript #113

Open hkarakurt8742 opened 3 years ago

hkarakurt8742 commented 3 years ago

As you know some variants have multiple NM_ coded transcripts. For example in this variant http://myvariant.info/v1/variant/chrX:g.153296529G>T, there are 7 different HGVS coding transcripts.

Is MyVariant.info have any system to choose the canonical transcripts? Which way would be better to follow for this kind of transcripts?

Thank you in advance

tdeboer-ilmn commented 2 years ago

Just looking for the answer to this question myself...Any way to find the canonical transcript for a gene? There are no obvious fields in MyGene.info where I would expect it...

newgene commented 2 years ago

@hkarakurt8742 this is how _id field in myvariant is defined:

https://docs.myvariant.info/en/latest/doc/data.html#id-field

when there is no proper mapping to chr, other HGVS names are used, e.g. some variants mapped only to the coding transcript not the genomic sequence yet.

This is certainly not a perfect system, and we are looking for a community-supported cannonical variant naming standard when it's available (e.g. https://github.com/biothings/myvariant.info/issues/108)

newgene commented 2 years ago

@tdeboer-ilmn "refseq.rna" field from MyGene.info?

http://mygene.info/v3/gene/1017?fields=refseq