ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7821C>T (p.Ser2607=) (rs532235331)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163955 SCV000214552 likely benign Hereditary cancer-predisposing syndrome 2014-12-04 criteria provided, single submitter clinical testing
Invitae RCV000198453 SCV000252595 benign Familial adenomatous polyposis 1 2017-12-27 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000310973 SCV000452049 likely benign APC-Associated Polyposis Disorders 2016-06-14 criteria provided, single submitter clinical testing
Counsyl RCV000198453 SCV000487782 likely benign Familial adenomatous polyposis 1 2015-11-24 criteria provided, single submitter clinical testing
GeneDx RCV000430616 SCV000512089 benign not specified 2015-05-21 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000430616 SCV000600162 benign not specified 2017-07-06 criteria provided, single submitter clinical testing
Color RCV000163955 SCV000681888 benign Hereditary cancer-predisposing syndrome 2016-11-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589014 SCV000694125 benign not provided 2016-07-01 criteria provided, single submitter clinical testing Variant summary: The APC c.7821C>T (p.Ser2607Ser) causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing, although 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 110/120952 (3 homozygotes, 1/1111), predominantly observed in the South Asian, 107/16502 (3 homozygotes, 1/154), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic APC variant of 1/14,0005 (0.0000714). Therefore, suggesting this variant is a common polymorphism found in population(s) of South Asian orign. The variant of interest, to our knowledge, has not been reported in affected individuals via publications, although multiple reputable clinical laboratories cite the variant as "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589014 SCV000888769 benign not provided 2017-07-06 criteria provided, single submitter clinical testing

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