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ACMG criteria that cannot be used together #4906

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dnil opened this issue Oct 3, 2024 · 0 comments · Fixed by #4932
Closed

ACMG criteria that cannot be used together #4906

dnil opened this issue Oct 3, 2024 · 0 comments · Fixed by #4932
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dnil commented Oct 3, 2024

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.

Certain ACMG criteria are not allowed together. In general one evidence should only count towards one term (eg PVS1 not together with PM4, which can be easily missed by the operator).

Describe the solution you'd like
Warn / flag when users fill in an incompatible combo.

Describe alternatives you've considered
It would be possible to forbid illegal ones. It is probably more flexible to just warn - eg gene specific criteria may say otherwise.
@dnil dnil self-assigned this Oct 8, 2024
dnil added a commit that referenced this issue Oct 10, 2024
@dnil
Fix #4906 - warn on potentially conflicting ACMG terms.
2f1f976
@dnil dnil mentioned this issue Oct 10, 2024
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@dnil dnil closed this as completed in 040862a Oct 11, 2024
dnil added a commit that referenced this issue Oct 11, 2024
@dnil @northwestwitch
Fix #4906 - warn on potentially conflicting ACMG terms. (#4932)
f1895ec 
* Fix #4906 - warn on potentially conflicting ACMG terms.

* add a tuple, sort, and simplify slightly

* add test

* typo

* Update scout/constants/acmg.py

Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>

* Update scout/utils/acmg.py

Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>

---------

Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
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Fix #4906 - warn on potentially conflicting ACMG terms. Clinical-Genomics/scout
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