ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4212C>T (p.Ser1404=) (rs144655979)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001078693 SCV000562666 likely benign Familial adenomatous polyposis 1 2020-11-25 criteria provided, single submitter clinical testing
Ambry Genetics RCV000492038 SCV000579832 likely benign Hereditary cancer-predisposing syndrome 2016-04-08 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Color Health, Inc RCV000492038 SCV000681657 likely benign Hereditary cancer-predisposing syndrome 2017-05-09 criteria provided, single submitter clinical testing
GeneDx RCV000615951 SCV000718252 likely benign not specified 2017-04-05 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000732075 SCV000859977 uncertain significance not provided 2018-03-07 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000615951 SCV001362430 likely benign not specified 2020-01-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000732075 SCV001549796 likely benign not provided no assertion criteria provided clinical testing The APC p.Ser1404Ser variant was not identified in the literature nor was it identified in the dbSNP, Genesight-COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, databases, but was identified in ClinVar (classified as likely benign by Invitae). The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project or the Exome Aggregation Consortium (August 8th 2016) control databases. The p.Ser1404Ser variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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