Classification rationale
1
The MSH2 c.793-11_794dup (NP_000242.1:p.?) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.
2
This variant is absent from gnomAD v2.1 and gnomAD v4.1; in gnomAD v4.1 the observed allele frequency is 0, which is below the MSH2 PM2_Supporting threshold of less than 0.00002.
3
SpliceAI predicts a splice effect with a maximum delta score of 0.71, which is above the MSH2 PP3 threshold of 0.2 for non-canonical splice variants and above the BP4 no-impact threshold of 0.1.
