Submissions for variant NM_000038.6(APC):c.532-8G>A

dbSNP: rs1060503323

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel	RCV003148748	SCV003836568	pathogenic	Familial adenomatous polyposis 1	2023-02-18	reviewed by expert panel	curation	The c.532-8G>A variant in APC is an intronic variant which is located 8 nucleotides upstream of the splice acceptor site for exon 6. This variant has been reported in 3 families meeting phenotypic criteria, resulting in a total phenotype score of 2.5 (PS4_Moderate; Ambry internal data; Invitae internal data; Leiden, Bonn, PMID 24599579; PMID19196998). This variant is absent from gnomAD v2.1.1 (PM2_supporting). The results from more than 2 in silico splicing predictors (SpliceAI, MaxEntScan, VarSeak) indicate that this variant may affect splicing by disrupting the acceptor splice site of intron 5 of APC (PP3). RT-PCR and minigene assay demonstrate that this variant impacts splicing by creating a novel splice acceptor site six nucleotides upstream of the regular splice acceptor site of exon 6 which results in the inclusion of six nucleotides including a premature termination codon. A complete splice defect was confirmed using transcript-specific PCR and SNP analysis of c.1458T>C (PS3_VeryStrong; PMID 19196998). In summary, this variant meets the criteria to be classified as Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS3_VeryStrong; PS4_moderate; PM2_supporting; PP3 (VCEP specifications version 1; date of approval: 12/12/2022).
Labcorp Genetics (formerly Invitae), Labcorp	RCV003148748	SCV000552641	likely pathogenic	Familial adenomatous polyposis 1	2020-11-02	criteria provided, single submitter	clinical testing	In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that this variant is associated with aberrant splicing resulting in the inclusion of the last 6 nucleotides of intron 4, which introduces a premature termination codon (PMID: 24599579). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant has been observed in individual(s) with familial adenomatous polyposis (PMID: 19196998). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 5 of the APC gene. It does not directly change the encoded amino acid sequence of the APC protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product.
Ambry Genetics	RCV000491376	SCV000579793	pathogenic	Hereditary cancer-predisposing syndrome	2015-09-16	criteria provided, single submitter	clinical testing	The c.532-8G>A intronic pathogenic mutation results from a G to A substitution 8 nucleotides before coding exon 5 in the APC gene. This mutation has been reported in an individual diagnosed with classic FAP at the age of 20 (Kaufamnn A et al. J Mol Diagn. 2009 Mar;11(2):131-9). In addition, in vivo and in vitro evidence demonstrated this alteration results in the creation of a new acceptor splice site leading to the inclusion of 6 additional intronic nucleotides encoding for a premature stop codon at codon 179 (p.S179X) (Kaufamnn A et al. J Mol Diagn. 2009 Mar;11(2):131-9; Grandval P, et al. Hum. Mutat. 2014 May; 35(5):532-6). This alteration was not reported in population-based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP) and 1000 Genomes Project. Based on nucleotide sequence alignment, this position is highly conserved in available vertebrate species. Based on the available evidence, c.532-8G>A is classified as a pathogenic mutation.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002298605	SCV002598594	likely pathogenic	Familial multiple polyposis syndrome	2022-09-06	criteria provided, single submitter	clinical testing	Variant summary: APC c.532-8G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Multiple computational tools predict a significant impact on normal splicing: Four predict the variant creates a cryptic 3' acceptor site, replacing the wildtype site and creating a premature stop codon. At least one publication reports experimental evidence that this variant affects mRNA splicing (Kaufmann_2009, Grandval_2014). The variant was absent in 247292 control chromosomes. c.532-8G>A has been reported in the literature in individuals affected with Familial Adenomatous Polyposis (Kaufmann_2009). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Myriad Genetics, Inc.	RCV003148748	SCV004044871	likely pathogenic	Familial adenomatous polyposis 1	2023-04-27	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 19196998].
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000503571	SCV000591038	likely pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The APC c.532-8G>A variant was identified by Kaufmann (2009) in a German individual with FAP. The variant was also identified InSiGHT Colon Cancer Gene Variant Database 3x as a splice mutation, and UMD (2x as a causal variant). The variant was not found in dbSNP, NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, Clinvitae database, COSMIC, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, “Zhejiang Colon Cancer Database”, the ClinVar database, or GeneInsight COGR database. The variant occurs outside of the splicing consensus sequence and 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. A functional study by Kaufmann (2009) found that the variant introduced a new splice acceptor site, creating a premature stop codon because of aberrant splicing producing an out-of-frame transcript. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as predicted pathogenic.