ACMG Variant Classification for Class II is inaccurate

[xiamaz]

Describe the bug Classifying a variant using benign criteria (BA/BS/BP) results in an wrong grade if 1 BS and 1 BP is used. According to Richards et al 2015 this should result in a likely benign classification, instead a variant of unknown significance is shown.

To Reproduce Steps to reproduce the behavior:

1. Filter variants in a single case or open Variant Annotation tab in a single case.
2. Click on 'singlevar-acmg-rating' button for a single variant.
3. Check 1 BS and 1 BP box.
4. Check the resulting automatic ACMG classification.

Expected behavior ACMG Class II should be shown in the automatic ACMG classification.

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows 10
• Browser Chrome

[xiamaz]

The classification is currently set here: https://github.com/bihealth/varfish-server/blob/4e3d07784f41d0c8cc9cc9d57df16c63a84fe830/varfish/static/js/flags_comments.js#L478

Changing this line to use 2 BP or 1 BS & 1 BP should fix the issue.

[holtgrewe]

Thanks, good catch. Will fix ASAP.