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bihealth / auto-acmg

Automatic classification of sequence variants and CNVs according to ACMG criteria.
GNU General Public License v3.0
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Termination positions for Frameshift/Nonesence SeqVars are not set properly #56

Closed gromdimon closed 5 months ago

gromdimon commented 7 months ago

Describe the bug In some decision blocks we rely on Termination position of the Variant if it's the frameshift/nonesence one. Currently we use pHGVS attribute for the determination of this, but due to many missing values of pHGVSs we have to find better approach to do this.

To Reproduce Example: NM_004360.3:c.2506G>T (p.Glu836Ter) (Gene: CDH1)
It gives the pHGVS result by Autopvs1 as NP_004351.1:p.Glu836Ter compare to one from mehari: 'NM_004360.5:p.?' this results in different results of termination position.

Expected behavior The termination positions should be computed in the unified way.

Screenshots N/A

Additional context It seems, that mehari lacks some data of pHGVS. In this case, we have to find an alternative way of findng the termination position.

Affected method: _get_pHGVS_termination

xiamaz commented 7 months ago

This looks like a mehari bug. Could you create an issue there? I'll try to prioritize it and perform root-cause analysis.

gromdimon commented 7 months ago

Here: https://github.com/varfish-org/mehari/issues/437

gromdimon commented 5 months ago

The issue is stilll on mehari site, but in auto-acmg it's outdated