You can test this further by just adding benign classifications and giving them strong modifiers. This results in pathogenic and likely_pathogenic outcomes. As I understand it, it's quite rare to have modifiers on benign classes but in this case, following the strict guidelines the geneticist came to this outcome.
We noticed when filling out the ACMG classifier that modifiers to benign classes would apply to the pathogenic terms as well.
We had this situation: PS3_moderate PP1_moderate PP3
This correctly defaults to uncertain significance. But, when adding a benign BS1_supporting
The classification instead turned into likely_pathogenic
It seems like this code snippet does not separate whether or not a term is of pathogenic origin or benign https://github.com/Clinical-Genomics/scout/blob/d448461287114e5a79d684ed2e67c913aea1906e/scout/utils/acmg.py#L193
You can test this further by just adding benign classifications and giving them strong modifiers. This results in pathogenic and likely_pathogenic outcomes. As I understand it, it's quite rare to have modifiers on benign classes but in this case, following the strict guidelines the geneticist came to this outcome.