ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2586C>G (p.Asn862Lys) (rs147972247)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120023 SCV000209502 likely benign not specified 2017-10-06 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.
Invitae RCV000200489 SCV000252911 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000290687 SCV000451997 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.
Ambry Genetics RCV000492033 SCV000579789 likely benign Hereditary cancer-predisposing syndrome 2018-09-14 criteria provided, single submitter clinical testing In silico models in agreement (benign);Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Other data supporting benign classification;General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Color RCV000492033 SCV000681536 likely benign Hereditary cancer-predisposing syndrome 2016-06-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590530 SCV000694014 benign not provided 2017-05-15 criteria provided, single submitter clinical testing Variant summary: The APC c.2586C>G (p.Asn862Lys) variant involves the alteration of a conserved nucleotide and 2/3 in silico tools (Mutation Taster and SNPsandGo not captured here due to low p-value and reliability index value, respectively) predict a benign outcome. However, these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 55/121326 (1/2206), predominantly in the South Asian cohort, 44/16508 (1/375), which does exceed the estimated maximal expected allele frequency for a pathogenic APC variant of 1/14005/ Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of South Asian origin. Multiple publications have cited the variant in affected individuals, although with limited information (ie, lack of cosegregation data). In addition, multiple clinical diagnostic laboratories classified this variant as "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Benign.
Counsyl RCV000200489 SCV000786296 likely benign Familial adenomatous polyposis 1 2018-04-05 criteria provided, single submitter clinical testing
ITMI RCV000120023 SCV000084153 not provided not specified 2013-09-19 no assertion provided reference population

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