ClinVar Miner

Submissions for variant NM_000038.6(APC):c.8043G>C (p.Pro2681=)

gnomAD frequency: 0.00092  dbSNP: rs149347068
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163472 SCV000214027 likely benign Hereditary cancer-predisposing syndrome 2015-01-13 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 RCV003534426 SCV000252596 benign Familial adenomatous polyposis 1 2024-02-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000371701 SCV000452053 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 RCV000163472 SCV000681906 benign Hereditary cancer-predisposing syndrome 2016-05-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590536 SCV000694134 benign not provided 2016-03-25 criteria provided, single submitter clinical testing Variant Summary: The c.8043G>C variant involves the alteration of a non-conserved nucleotide resulting in a synonymous change. 3/5 in silico tools via Alamut predict no significant effect on splicing. The variant was observed in the large, broad control population, ExAC with, an allele frequency of 0.025%, primarily observed in the African subpopulation at a frequency of 0.27%. This frequency exceeds the maximum expected allele frequency for a pathogenic APC variant of 0.006%, suggesting this is a benign polymorphism found primarily in the African subpopulation. Multiple reputable clinical labs have classified the variant as likely benign/benign. Taken together, due to the synonymous nature of the variant, the relatively high frequency of the variant in the population, and the lack of predicted effect on splicing, this variant has been classified as Benign.
Preventiongenetics, part of Exact Sciences RCV000590536 SCV000805475 likely benign not provided 2017-12-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000590536 SCV000888773 benign not provided 2023-05-17 criteria provided, single submitter clinical testing
GeneDx RCV000590536 SCV001865589 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000163472 SCV002531515 benign Hereditary cancer-predisposing syndrome 2020-10-30 criteria provided, single submitter curation
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000590536 SCV003799434 benign not provided 2022-11-28 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV002516450 SCV004015947 benign Familial adenomatous polyposis 1 2023-07-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000590536 SCV004159233 likely benign not provided 2022-11-01 criteria provided, single submitter clinical testing APC: BP4, BP7, BS1

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