APC p.Ser634Arg

The NM_000038.6(APC):c.1902T>G (p.Ser634Arg) variant in APC is a missense variant predicted to cause substitution of Serine by Arginine at amino acid position 634 (p.Ser634Arg). This variant has been reported in 1 proband meeting phenotypic criteria, resulting in a total phenotype score of 0.5 (PS4 not met [Ambry]). The variant has been reported in 1 additional proband with a colorectal cancer/polyposis associated phenotype not meeting phenotypic criteria (PMID: 27696107). The total minor allele frequency in gnomAD v2.1.1 (non-cancer) is 0.0004% (1/236788 alleles), which is lower than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP (HCCP VCEP) threshold < 0.001% (0.00001) for PM2_Supporting if the allele count is ≤ 1 and therefore meets this criterion (PM2_Supporting). RT-PCR of cDNA and mini-gene splicing assays demonstrated that the variant impacts splicing by skipping of exon 15 resulting in a premature stop codon (PMID: 24599579). However, since alternative splicing/skipping of this exon is known and in PMID: 24599579 no pronounced skipping compared to controls is described, PS3 is not applicable. Moreover, the results from ≥ 2 in silico splicing predictors (SpliceAI and MaxEntScan) support that this variant does not affect splicing. APC, in which the variant was identified, is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). Due to conflicting evidence, this variant is a variant of uncertain significance (VUS) for autosomal-dominant inherited FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: PM2_Supporting, BP1 (VCEP specifications version v2.0.3; date of approval 7/24/2023).