wrightmw
commented
3 years ago The Total Points reflects all default points for variants, but the Points Counted shows combined points for variants (and maxes out at 12 too), so this looks like it isn't an issue that effects the scoring/classification. Alternatively, we should look into better messaging in the Classification Matrix to make this clearer to users.
In the SOPv8 scoring system for variants, the scores for two autosomal recessive variants in one proband are combined together... but...the combined score for a variant pair should max out at 3. This is happening correctly when the variants are added and scored, but in the classification matrix sometimes the combined maxed out scores of 3 are not being summed into the Total Points, but instead the scores for each individual variant are being summed. For example in PPT1 - neuronal ceroid lipofuscinosis 1, the combined score for each variant pair would be 3 and there are 6 variant variant pairs, so it should be 3 x 6 = 18, however instead it shows 24 as the total, which would indicate that it is instead summing the 2 points per individual variant instead, i.e. 2 x 12 = 24