ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1685C>T (p.Thr562Met)

gnomAD frequency: 0.00002  dbSNP: rs587783034
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000222854 SCV000274259 benign Hereditary cancer-predisposing syndrome 2023-01-12 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp RCV000144570 SCV000282700 likely benign Familial adenomatous polyposis 1 2024-01-19 criteria provided, single submitter clinical testing
GeneDx RCV000766534 SCV000569774 uncertain significance not provided 2024-04-08 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with colorectal cancer (PMID: 28944238); This variant is associated with the following publications: (PMID: 18199528, 28944238, 36243179)
Color Diagnostics, LLC DBA Color Health RCV000222854 SCV000681482 uncertain significance Hereditary cancer-predisposing syndrome 2023-01-24 criteria provided, single submitter clinical testing This missense variant replaces threonine with methionine at codon 562 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with colorectal cancer (PMID: 28944238). This variant has been identified in 16/282672 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000485323 SCV000731502 uncertain significance not specified 2017-03-20 criteria provided, single submitter clinical testing The p.Thr562Met variant in APC has not been previously reported in individuals w ith familial adenomatous polyposis or other APC-associated disorders but has bee n reported in ClinVar (Variation ID: 156480). It has also been identified in 2/8 618 of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs587783034). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Thr562Met variant is uncertain.
Counsyl RCV000144570 SCV000785064 uncertain significance Familial adenomatous polyposis 1 2017-04-04 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000144570 SCV004018741 likely benign Familial adenomatous polyposis 1 2023-02-17 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.
All of Us Research Program, National Institutes of Health RCV003998159 SCV004837430 uncertain significance Classic or attenuated familial adenomatous polyposis 2023-12-01 criteria provided, single submitter clinical testing This missense variant replaces threonine with methionine at codon 562 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in an individual affected with colorectal cancer (PMID: 28944238). This variant has been identified in 16/282672 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and in healthy control individuals (PMID: 32980694). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Pathway Genomics RCV000144570 SCV000189866 uncertain significance Familial adenomatous polyposis 1 2014-07-24 no assertion criteria provided clinical testing

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