ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5790A>G (p.Gln1930=) (rs141152252)

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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 RCV000163473 SCV000214028 likely benign Hereditary cancer-predisposing syndrome 2015-01-13 criteria provided, single submitter clinical testing
Invitae RCV001084355 SCV000252590 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000328659 SCV000452029 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.
GeneDx RCV000444405 SCV000512079 benign not specified 2015-05-14 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 RCV000444405 SCV000600119 likely benign not specified 2017-02-22 criteria provided, single submitter clinical testing
Color RCV000163473 SCV000681761 benign Hereditary cancer-predisposing syndrome 2016-05-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586171 SCV000694086 benign not provided 2016-03-25 criteria provided, single submitter clinical testing Variant summary: c.5790A>G affects a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts benign outcome. 3/5 in silico programs via Alamut predict no significant change on RNA splicing sites. ESEfinder predicts a gain of binding motif for RNA splicing enhancer SC35. This variant was found in 30/120712 control chromosomes at a frequency of 0.0002485, which is more than 3 times of maximal expected frequency of a pathogenic allele (0.0000602), suggesting this variant is benign. In addition, multiple clinical laboratories classified this variant as benign/likely benign. Taken together, this variant was classified as Benign.
PreventionGenetics,PreventionGenetics RCV000586171 SCV000805439 likely benign not provided 2017-12-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586171 SCV000888749 benign not provided 2018-04-28 criteria provided, single submitter clinical testing

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