APC p.Arg348Ter

The NM_000038.6(APC):c.1042C>T variant in APC is predicted to cause a premature stop codon (p.R348Ter) located between codon 49 and 2645 in biologically relevant exon 10 (coding exon 9) in a gene in which loss-of-function is an established disease mechanism. However, based on unpublished RNA analyses from Ambry Genetics, the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP (HCCP VCEP) does not consider this variant to be applicable to PVS1. The RNA analyses showed that this variant results in an in-frame aberrant transcript lacking part of exon 10 [r.934_1074del (p.V312_Q358del)]. In addition, an increased expression of a naturally occurring alternative transcript (r.934_1236del (p.V312_Q412del), known as “exon 9a”) was observed relative to controls. The predicted premature stop codon (p.R348Ter) was excluded from both the aberrant and naturally occurring transcripts and might provide a rescue mechanism for this nonsense alteration. The total minor allele frequency in gnomAD v2.1.1 (non-cancer) is 0.000004 (1/251004 alleles), which is lower than the HCCP VCEP threshold 0.00001 for PM2_Supporting if the allele count is ≤ 1 and therefore meets this criterion (PM2_Supporting). This variant has been reported in three families with a polyposis phenotype, resulting in a total phenotype score of 1.5 points (PS4_Supporting, [PMID: 11754114 and 12007223; CanVIG-UK]). On the other hand, this variant has been observed in heterozygous state in 7 healthy unrelated adult individuals worth ≥ 6 healthy individual points in total (BS2_Supporting; [Ambry Genetics, Invitae, UK Biobank, 100,000 Genomes Project]). Due to conflicting evidence, this variant is classified as a variant of uncertain significance (VUS) for autosomal-dominant inherited FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: criteria PS4_Supporting, PM2_Supporting and BS2_Supporting applied (VCEP specifications version 2.0.3; date of approval 7/24/2023).