LMNA variant incorrectly classified

[pnrobinson]

In the GPSEA-CS analysis of LMNA, we have the following issue (note that the analysis itself is working, the only problem is a small one in the Variant Allele table that is produced by

from gpsea.view import CohortVariantViewer

viewer = CohortVariantViewer(tx_id=mane_tx_id)
viewer.process(cohort)

GRCh38:1:156138613:C:T is NM_170707.4:c.1824C>T
According to VariantValidator we have NP_733821.1:p.(Gly608=) -- this is correct (see https://www.ncbi.nlm.nih.gov/clinvar/variation/14500/)

However, our variant allele shows this as downstream of gene

It should be listed as synonymous (the actual effect is on splicing, but there is no way the software can deduce that; ideally it would say splicing region variant).

[ielis]

We delegate the functional annotation to Ensembl's VEP REST API. I am not sure there is anything we can do here.