Add ACMG CNV criteria to rules engine
Background
Add support for ACMG CNV criteria in rules engine.
Implementation
There are two major tasks here:
1. Generate suggestions for individual scores
A quick solution could be to use AnnotSV prediction (based on the annotation from AnnotSV), which provides output for most of section 1-3 in the ACMG CNV guidelines. The alternative is to implement similar rules ourselves.
2. (most important) Calculate final score and suggest classification
This should be a simple task, just add together any scores the user has committed (see #263; as opposed to suggested scores) and generate a suggestion for classification based on these rules:
Final point value | Class |
---|---|
≥0.99 | Pathogenic |
0.90 - 0.98 | Likely pathogenic |
-0.89 - 0.89 | VUS |
-(0.90 - 0.98) | Likely benign |
≤-0.99 | Benign |
Important note: AnnotSV provides a suggested classfication based on the suggested criteria. However, these do not cover all sections in the ACMG CNV guidelines, and should therefore not be used for generating the final score to be committed in VarDB, but instead only display the score as a suggested result.