ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7490C>T (p.Ser2497Leu) (rs141010008)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000122800 SCV000166057 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000131590 SCV000186602 benign Hereditary cancer-predisposing syndrome 2015-09-12 criteria provided, single submitter clinical testing Does not segregate with disease in family study (genes with incomplete penetrance);Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign);General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
GeneDx RCV000120032 SCV000209549 likely benign not specified 2017-10-04 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.
Integrated Genetics/Laboratory Corporation of America RCV000587624 SCV000694118 benign not provided 2016-03-25 criteria provided, single submitter clinical testing Variant Summary: The c.7490C>T variant involves the alteration of a conserved nucleotide and 3/4 in silico tools predict a neutral outcome. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.033%, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.055%. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in APC (0.006%), suggesting this is a benign polymorphism found primarily in population(s) of European origin. The variant was reported in a family affected by multiple colorectal adenomas and carcinoma, however was absent in two affected members and was present in 3 unaffected members, showing lack of segregation of the variant with disease (Al-Tassan_2002). While one reputable clinical lab has classified the variant as likely benign, others have classified it as a VUS. Considering the relatively high frequency of this variant in the general population as well as the lack of segregation seen in an affected family, this variant has been classified as Benign.
Mendelics RCV000122800 SCV000838150 uncertain significance Familial adenomatous polyposis 1 2018-07-02 criteria provided, single submitter clinical testing
Color RCV000131590 SCV000910611 benign Hereditary cancer-predisposing syndrome 2016-03-22 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587624 SCV001133368 likely benign not provided 2019-01-24 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000587624 SCV001154481 likely benign not provided 2018-04-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001153055 SCV001314303 likely benign APC-Associated Polyposis Disorders 2019-02-19 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
ITMI RCV000120032 SCV000084163 not provided not specified 2013-09-19 no assertion provided reference population

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