ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6921G>A (p.Ser2307=) (rs2229993)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000211932 SCV000167014 benign not specified 2014-01-06 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 RCV000128942 SCV000172817 benign Hereditary cancer-predisposing syndrome 2014-12-13 criteria provided, single submitter clinical testing Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene;General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Invitae RCV001083611 SCV000252592 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000398735 SCV000452042 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.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000211932 SCV000591205 benign not specified 2015-06-10 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000211932 SCV000593258 likely benign not specified 2017-04-27 criteria provided, single submitter clinical testing
Color RCV000128942 SCV000681834 benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586387 SCV000694103 benign not provided 2016-02-23 criteria provided, single submitter clinical testing Variant summary: The APC c.6921G>A variant affects a non-conserved nucleotide, resulting in a synonymous change at Ser2307. 5/5 Alamut algorithms predict no significant change to normal splicing. ESEfinder predicts a loss of binding motif for RNA splicing enhancer. These in silico predictions have not been verified with in vitro/in vivo functional studies. This variant was found in 169/120898 control chromosomes at a frequency of 0.0013979, which is about 23 times the maximal expected frequency of a pathogenic APC allele (0.0000602), suggesting this variant is benign. In addition, multiple clinical laboratories database classified this variant as benign. Taken together, this variant was classified as benign.
PreventionGenetics,PreventionGenetics RCV000211932 SCV000805459 benign not specified 2017-03-03 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000586387 SCV001154479 likely benign not provided 2019-10-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000211932 SCV001156604 benign not specified 2019-01-30 criteria provided, single submitter clinical testing
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000211932 SCV000691761 likely benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000128942 SCV000693487 likely benign Hereditary cancer-predisposing syndrome 2017-09-11 no assertion criteria provided clinical testing

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