hgvs_p shows Ter, although no new stop codon got introduced.

[andreasprlic]

Hi,

Looks like the following code results in a slightly incorrect hgvs_p string:

In [1]: hgvs_c = 'NM_002485.4:c.2256_2258del'
In [2]: var_c = parse(hgvs_c)
In [3]: c_to_p(var_c)
Out[3]: SequenceVariant(ac=NP_002476.2, type=p, posedit=(Arg754Ter), gene=None)

I would expect that the created variant is actually Arg754del, rather than Ter, since no new stop codon got introduced.

Here the environment for this variant:

Note: this is a reverse strand transcript, as such the protein sequence needs to get read from right->left, but the displayed genomic reference sequence is forward strand.

Another note: I believe this is Arg754del, rather than Arg752del or Arg753del, since the HGVS spec suggests that all (protein) reference sequences need to get described in the most C-terminal possible position.

[github-actions[bot]]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been stalled for 7 days with no activity.

[reece]

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.