Genetic Evidence Scoring System Revamp and Variant Evaluation Guidelines

Gene Curation SOP v8 Overview of Updates

Main Update: Revamp of Genetic Evidence Scoring System Issues: Need to downgrade missense variants without functional data unclear No distinction between types of de novo variants Distinct values for LOF and de novo variants in AD/X inheritance but not AR Category maximums penalizing non-LOF disease mechanisms SOP v7

Main Update: Revamp of Genetic Evidence Scoring System New! Baseline points assigned per variant type Add points to baseline for common upgrades No category maximums SOP v8

Always check with your GCEP to determine final variant scoring. Let this framework serve as a GUIDE.

Case-Level Variant Evidence Baseline number of points assigned per variant type Predicted/proven null = 1.5 points Other variant type (e.g., missense) = 0.1 points Add points to the baseline score for common upgrades as described in the table Functional data De novo status Other upgrades/downgrades may be appropriate at the discretion of your GCEP

Case-Level Variant Evidence For AR diseases: assess each variant independently, then sum for final score Round up to the nearest 0.5 EXCEPTION: For 2 missense variants w/o functional data, round to 0.25 No single proband may score more than 3 points

Caveats Default scores assume the variant type is consistent with the expected disease mechanism. If this is not the case, downgrade or do not score unless there is compelling rationale for partial scoring. Document this rationale in the GCI. For example, if the disease mechanism is known to be gain of function, consider not scoring null variants and upgrading gain of function missense variants. Variants may be up- or downgraded beyond the values suggested here (but within the scoring range) based on the strength of evidence. For example, a missense variant may score at the top of its range if robust functional assays demonstrate that the missense is acting in a manner consistent with the expected disease mechanism.

Caveats Variants may be up- or downgraded for other reasons beyond those listed in this chart at the discretion of the GCEP. Always document the rationale for up- or downgrading variants in the GCI. For example, one may opt to upgrade missense variants if they are within a known functional domain, if they appear to be clustering in the same area of the gene, etc. Consider upgrading based on consistency and/or specificity of the phenotype, the likelihood that a putative null variant actually leads to loss of function, etc. When assigning points for de novo status, consider further upgrades if statistical evidence shows that de novo variation in a particular gene is rare. Use caution (and consider not upgrading or not scoring) if a gene is known to have a high rate of de novo variation (e.g. TTN).

AD/XL Inheritance Example Scenarios 1 missense variant with no functional data = baseline 0.1 points Add functional data (0.1 + 0.4) = 0.5 points Add de novo status (0.1 + 0.4) = 0.5 points Add both (0.1 + 0.4 + 0.4) = 0.9 round to the nearest 0.5 = 1 point 1 LOF variant = baseline 1.5 points Add functional data (1.5 + 0.5) = 2 points Add de novo status (1.5 + 0.5) = 2 points Add both (1.5 + 0.5 +0.5) = 2.5 points

AD/XL Inheritance Example Scenarios 1 missense variant with no functional data = baseline 0.1 points Add functional data (0.1 + 0.4) = 0.5 points Add de novo status (0.1 + 0.4) = 0.5 points Add both (0.1 + 0.4 + 0.4) = 0.9 round to the nearest 0.5 = 1 point 1 LOF variant = baseline 1.5 points Add functional data (1.5 + 0.5) = 2 points Add de novo status (1.5 + 0.5) = 2 points Add both (1.5 + 0.5 +0.5) = 2.5 points

AR Inheritance Example Scenarios Score for Variant 1 + Score for Variant 2 = Final Score Round to nearest 0.5 EXCEPT for 2 missense w/o functional data (round to 0.25) Example: Variant 1 is a missense variant w/o functional data. Variant 2 is a de novo LOF variant Variant 1 = 0.1 points Variant 2 = 1.5 + 0.5 = 2 points Total score: 0.1 + 2 = 2.1 round down to 2 points

AR Inheritance Example Scenarios Score for Variant 1 + Score for Variant 2 = Final Score Round to nearest 0.5 EXCEPT for 2 missense w/o functional data (round to 0.25) Example: Variant 1 is a missense variant with functional data. Variant 2 is a de novo missense variant Variant 1 = 0.1 + 0.4 = 0.5 points Variant 2 = 0.1 + 0.4 = 0.5 points Total score: 0.5 + 0.5 = 1 point

AR Inheritance Example Scenarios Score for Variant 1 + Score for Variant 2 = Final Score No single proband can score more than 3 points Example: Variant 1 is a LOF variant with functional data. Variant 2 is a de novo LOF variant Variant 1 = 1.5 + 0.5 = 2 points Variant 2 = 1.5 + 0.5 = 2 points Total score: 2 + 2 = 4 points CAP AT 3 POINTS

Entering this information in the GCI The GCI will not immediately reflect this change in scoring organization. At this time, you will still need to select from the old variant scoring categories (e.g., LOF, de novo, etc.) The defaults programmed into the GCI may not reflect the recommended scoring per SOP v8 you may need to adjust. In addition to any notes you normally would make, you can include Adjusted default scoring per recommendations in SOP v8 in the Reason for changed score field. The GCI team is working on the necessary updates to enable this scoring.

Other changes Reminder to groups to enter gene/disease/MOI and any precuration information into the GeneTracker Current work-around for including large, intragenic CNVs in curation Evidence summaries are now REQUIRED

Reminder: Enter all gene lists, precuration information, etc. into Gene Tracker

Including intragenic CNVs in a curation

Evidence summaries are now REQUIRED Will discuss more on a future Biocurator call