Figure 6.

Screenshot of SQUIRLS HTML output

The variant GenBank: NM_000249.3; c.86C>G generates a cryptic splice site in MLH1 (MIM: 120426).⁴⁹ The variant is evaluated with respect to four overlapping transcripts and it is assigned maximum SQUIRLS score = 0.893. Transcripts with predicted maximum SQUIRLS score are highlighted in the table. The variant is located 31 bp upstream of the canonical site of exon 1 and it is predicted to create a cryptic donor site (R_i = 8.19 bits) which is stronger than the canonical donor (R_i = 6.17 bits) by 2.02 bits. Using the cryptic donor site would lead to removal of 31 bases from the coding sequence. Bar charts compare the canonical donor site with the predicted cryptic site. The bar chart shows that the variant replaces cytosine (blue rectangle) with a guanine (orange rectangle). The change is predicted to allow a more favorable contact between spliceosome and the alt allele, resulting in usage of the cryptic site and removing 31 bases from the coding sequence.