ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7201C>T (p.Leu2401=)

gnomAD frequency: 0.01134  dbSNP: rs2229994
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Total submissions: 22
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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 RCV000035082 SCV000058722 benign not specified 2012-04-24 criteria provided, single submitter clinical testing Leu2401Leu in exon 15 of APC: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 1.3% (92/7020) of Eu ropean American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS/; rs2229994).
Invitae RCV003650361 SCV000153892 benign Familial adenomatous polyposis 1 2024-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000128900 SCV000172761 benign Hereditary cancer-predisposing syndrome 2014-10-22 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.
Eurofins Ntd Llc (ga) RCV000035082 SCV000226393 benign not specified 2014-08-04 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000303809 SCV000452043 benign APC-Associated Polyposis Disorders 2018-01-13 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.
Color Diagnostics, LLC DBA Color Health RCV000128900 SCV000537383 benign Hereditary cancer-predisposing syndrome 2016-03-17 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000755461 SCV000602509 benign not provided 2023-11-30 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000035082 SCV000805462 benign not specified 2016-12-16 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000755461 SCV001133362 benign not provided 2019-05-07 criteria provided, single submitter clinical testing
GeneDx RCV000755461 SCV001828324 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000128900 SCV002527512 benign Hereditary cancer-predisposing syndrome 2021-05-11 criteria provided, single submitter curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000035082 SCV002550651 benign not specified 2023-08-15 criteria provided, single submitter clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000128900 SCV002819193 benign Hereditary cancer-predisposing syndrome 2022-09-27 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV002513347 SCV004017527 benign Familial adenomatous polyposis 1 2023-07-07 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353597 SCV000591206 benign Carcinoma of colon no assertion criteria provided clinical testing The p.Leu2401Leu 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 the dbSNP database as coming from a "clinical source" (ID#: rs2229994) with an average heterozygosity of 0.022+/-0.103, therefore increasing the likelihood of this variant to be benign. It has been identified in our laboratory in one among the 973 individuals who have undergone APC testing. Additionally, it has been identified twice in the literature, in 2/258 (0.007% frequency) proband chromosomes and 1/1052 (0.001 frequency) control chromosomes where it was classified as a polymorhism (Hadjisavvas_2006_16650078, Zhou_2004_15122587). In summary, based on the above information, the p.Leu2401Leu variant is classified as predicted benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000035082 SCV000691763 benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000128900 SCV000693489 likely benign Hereditary cancer-predisposing syndrome 2017-11-10 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000035082 SCV001797677 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000035082 SCV001807005 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000035082 SCV001920369 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000035082 SCV001954359 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000035082 SCV001965728 benign not specified no assertion criteria provided clinical testing

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