ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4479G>A (p.Thr1493=)

gnomAD frequency: 0.59177  dbSNP: rs41115
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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000035071 SCV000058711 benign not specified 2020-07-27 criteria provided, single submitter clinical testing The p.Thr1493Thr variant in APC is classified as benign because it has been identified in 82% (16364/19946) of East Asian chromosomes, including 6724 homozygotes, by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1.
Eurofins Ntd Llc (ga) RCV000035071 SCV000109824 benign not specified 2016-03-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162372 SCV000212682 benign Hereditary cancer-predisposing syndrome 2014-10-31 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: 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.
Preventiongenetics, part of Exact Sciences RCV000035071 SCV000301595 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000383485 SCV000452013 benign APC-Associated Polyposis Disorders 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001636617 SCV000602515 benign not provided 2023-11-29 criteria provided, single submitter clinical testing
Invitae RCV003315552 SCV000647520 benign Familial adenomatous polyposis 1 2024-02-01 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000162372 SCV000681669 benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
GeneDx RCV001636617 SCV001847829 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002496525 SCV002808339 benign Desmoid disease, hereditary; Familial adenomatous polyposis 1; Hepatocellular carcinoma; Gastric cancer; Colorectal cancer; Gastric adenocarcinoma and proximal polyposis of the stomach 2022-05-24 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003315552 SCV004017438 benign Familial adenomatous polyposis 1 2023-07-07 criteria provided, single submitter clinical testing
Systems Biology Platform Zhejiang California International NanoSystems Institute RCV000074234 SCV000105827 cancer Familial colorectal cancer no assertion criteria provided not provided Converted during submission to other.
Mayo Clinic Laboratories, Mayo Clinic RCV000035071 SCV000256997 benign not specified no assertion criteria provided research
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353469 SCV000591174 benign Carcinoma of colon no assertion criteria provided clinical testing The c.4479G>A, p.Thr1493Thr variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located near a splice junction, and is listed in dbSNP (rs_id: rs41115) as a common polymorphism with a global minor allele frequency of 0.338. It has not been previously identified by our laboratory, but has been reported in the literature in 72/2142 (frequency of 0.033) proband chromosomes from individuals with familiar adenamatous polyposis, colorectal carcinoma, papillary thyroid carcinoma and sporadic ependymoma. It has also been identified in 54/2322 (frequency of 0.023) control chromosomes, increasing the likelihood that the variant has no clinical significance (Rocco_2006, Azzopardi_2008_18199528, Chao_2006_16569251, Curia_2012_21995949, Jasperson_2010_20420945, Kamory_2008_18369740, Onilude_2006_16843107, Schwab_2008_18026870, Subramaniam_2007_18024325, Teijeiro_2009_19095577). In summary, based on the above information, this variant is classified as benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000035071 SCV001742783 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000035071 SCV001922241 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000035071 SCV001953579 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000035071 SCV001971880 benign not specified no assertion criteria provided clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000162372 SCV002050302 benign Hereditary cancer-predisposing syndrome 2021-12-21 no assertion criteria provided clinical testing

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