ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1554G>A (p.Thr518=) (rs546568052)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000586072 SCV000166016 benign not provided 2019-02-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162691 SCV000213145 likely benign Hereditary cancer-predisposing syndrome 2014-07-30 criteria provided, single submitter clinical testing
GeneDx RCV000435025 SCV000512063 likely benign not specified 2017-09-01 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.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000435025 SCV000591078 benign not specified 2015-12-15 criteria provided, single submitter clinical testing
Color RCV000162691 SCV000681473 benign Hereditary cancer-predisposing syndrome 2016-05-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586072 SCV000694000 benign not provided 2016-05-03 criteria provided, single submitter clinical testing Variant summary: The APC variant, c.1554G>A (p.Thr518Thr) causes a synonymous change involving a non-conserved nucleotide with 5/5 in silico tools via Alamut predict no significant effect 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 122/120352 (1/986 including 2 homozygotes), predominantly in the South Asian cohort, 119/16346 (1/137 including 2 homozygotes), which exceeds the estimated maximum expected allele frequency for a pathogenic APC variant of 1/16611. Therefore, suggesting that the variant of interest is a common polymorphism found in population(s) of South Asian origin. It was reported once in a patient with another causative mutation that is not specified (Scott_Hered Cancer Clin Prac_2004). Multiple reputable clinical laboratories cite the variant with a classification of "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

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