GCI: Score homozygous probands at 0.1.

[bmpbowen]

Request from Gene Curation Small Group:

Add a 0.05 option to the GCI for homozygous probands, and include a tooltip to explain that homozygous probands get scored as 0.1

[bmpbowen]

[gcheung-SF]

Questions:

1. So 0.05 score option is only available in following condition: Variant Type = Other Variant Type de novo = No Function Data = No But not for other combinations (i.e. de novo = Yes)? And the tooltip appears all the time or when user selects above and 0.05 point?

2. When MOI = Semidominant inheritance and proband is = "Biallelic homozygous" or "Biallelic compound heterozygous" then treat as AUTOSOMAL_RECESSIVE. If user checks homozygous box, should same logic apply at this case?

[bmpbowen]

My apologies for the confusion generated by the sample screenshot. To answer the above questions:

1. I think we want the 0.05 option to appear for all homozygous variant types, not just "other variant type".

• Re: de novo, most de novo variants occur in AD conditions in the heterozygous state. I don't think we would score a homozygous de novo variant but I'll confirm with the gene curation small group since there can be some very rare edge cases where one might think one or both of a proband's variants occurred de novo. They said it would be simplest to just leave the 0.05 option across all scenarios
• Re: functional data... functional data should not impact whether the 0.05 option applies.
• Tooltip: we want it there all the time.

3. When MOI - Semidominant and proband is biallelic homozygous or biallelic compound heterozygous, we also want to include the 0.05 scoring option.

[gcheung-SF]

Changes is now on live site.