[GET-dev] Autoscoring

Madeleine Price Ball meprice at gmail.com
Thu May 20 14:20:07 EDT 2010

The current plan is to have an autoscoring tool that it produces up to
6 points for a variant. Although we thought we'd initialize the
scoring on the GET-Evidence pages themselves, I think (at least at the
moment) we should not plan on this -- but we still want to generate a
score within the system associated with the variant. We can use that
score to sort variants that have insufficient evaluation for further

The plan:

Autoscoring is split into three sections: computational,
variant-specific, and gene-specific, each 2 points for a max of 6

Computational (max of 2 points):
If an non-synonymous substitution:
+1 for NBLOSUM >= 3,
another +1 (+2 total) if NBLOSUM = 10 (a nonsense mutation)
For all variants:
+1 if within 1 base of a splice site
(Trait-o-matic has splicing data, presumably it could spot these?)
+1 for indel in coding region
another +1 (+2 total) if causes a frameshift (not a multiple of 3 in
coding region)

Variant-specific lists (max of 2 points):
+2 if in OMIM
+1 if in PharmGKB
+1 if in HuGENet
another +1 (+2 total) if HuGENet's OR >= 1.5

Gene-specific lists (max of 2 points):
+1 if in GeneTests
another +1 (+2 total) if in a GeneReviews gene

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