ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2805C>T (p.Tyr935=) (rs137854575)

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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000211904 SCV000167003 benign not specified 2014-05-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000123663 SCV000213569 likely benign Hereditary cancer-predisposing syndrome 2014-08-29 criteria provided, single submitter clinical testing This alteration is classified as likely 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.
Invitae RCV000987567 SCV000252581 benign Familial adenomatous polyposis 1 2020-12-07 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000202773 SCV000257783 likely benign Familial multiple polyposis syndrome 2015-07-10 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000211904 SCV000538291 likely benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent, ClinVar: variant classified as benign by 2 labs; ExAC: 0.1% (51/66634) European chromosomes
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000211904 SCV000602527 benign not specified 2018-08-29 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123663 SCV000681552 likely benign Hereditary cancer-predisposing syndrome 2016-03-17 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000679052 SCV000805385 likely benign not provided 2018-01-22 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679052 SCV000887511 benign not provided 2018-09-08 criteria provided, single submitter clinical testing
Mendelics RCV000987567 SCV001136899 likely benign Familial adenomatous polyposis 1 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000679052 SCV001154459 likely benign not provided 2021-04-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001157045 SCV001318591 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001354034 SCV000591120 benign Carcinoma of colon no assertion criteria provided clinical testing The APC p.Tyr935Tyr variant was identified in dbSNP (ID: rs137854575) “With Pathogenic allele”, with a minor allele frequency of 0.0004 (1000 Genomes Project), NHLBI Exome Sequencing Project (Exome Variant Server) and the ClinVar database (classified as a benign variant by GeneDX). The variant was identified by the Exome Variant Server project in 5 of 13004 European American and African American alleles (frequency: 0.0004), although this low number of observations and low frequency is not substantive enough to determine the prevalence of the variant in the general population and its relationship to disease.The p.Tyr935Tyr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000211904 SCV000691726 likely benign not specified no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000211904 SCV001918785 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000679052 SCV001952609 likely benign not provided no assertion criteria provided clinical testing

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