missing hgvs_c when indel is realigned and shifted.

[sicotte]

I noticed a lot of indels/fs have missing hgvs_c NM transcript information. I do see the hgvs_p (with the protein),

Example:
This variant
https://www.ncbi.nlm.nih.gov/clinvar/variation/52203/

is listed as Chr13: 32341188 – 32341192 in clinvar

In the files from the clinvar/macarthur pipeline,
It gets left shifted here: 13 32341183

There is no “hgvs_c” field in the output from the pipeline
It does have have (which is the same as clinvar .. not sure if that was recomputed).
"hgvs_p":"NP_000050.2:p.Ile2278Serfs",

However, we can find the hgvs_c information under the molecular consequence field.

"molecular_consequence":["NM_000059.3:c.6833_6837del:frameshift variant"]

I’m not sure if the pipeline computed that or it’s from clinvar (same as in clinvar)..
But it could be propagated to the hgvs_c field.