ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6387G>A (p.Ser2129=) (rs374310157)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163062 SCV000213556 likely benign Hereditary cancer-predisposing syndrome 2014-12-09 criteria provided, single submitter clinical testing
Invitae RCV001083836 SCV000252591 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000293113 SCV000452034 likely benign APC-Associated Polyposis Disorders 2016-06-14 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000508036 SCV000600124 likely benign not specified 2017-01-25 criteria provided, single submitter clinical testing
Color RCV000163062 SCV000681797 benign Hereditary cancer-predisposing syndrome 2016-05-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589653 SCV000694091 benign not provided 2017-01-26 criteria provided, single submitter clinical testing Variant summary: The APC c.6387G>A (p.Ser2129Ser) variant causes a synonymous change involving a non-conserved nucleotide, 4/5 splice prediction tools predict no significant impact on normal 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 34/121086 (1/3561), predominantly in the Latino cohort, 30/11544 (1/384), which significantly exceeds 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 Latino origin. The variant of interest has not been, to our knowledge, reported in affected individuals via publications, although multiple clinical diagnostic laboratories cite the variant with a classification of "likely benign/benign." Therefore, the variant of interest has been classified as Benign.

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