ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5304G>A (p.Lys1768=) (rs863224285)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000200536 SCV000252931 likely benign Familial adenomatous polyposis 1 2020-12-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000570509 SCV000667346 likely benign Hereditary cancer-predisposing syndrome 2015-09-17 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000608378 SCV000694073 likely benign not specified 2019-08-20 criteria provided, single submitter clinical testing
GeneDx RCV000608378 SCV000716616 likely benign not specified 2017-03-03 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.
Color Health, Inc RCV000570509 SCV000906744 likely benign Hereditary cancer-predisposing syndrome 2018-11-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357058 SCV001552391 uncertain significance not provided no assertion criteria provided clinical testing The APC p.Lys1768= variant was not identified in the literature nor was it identified in the following databases: COGR, Cosmic, MutDB, LOVD 3.0, or the Zhejiang Colon Cancer Database. The variant was identified in dbSNP (ID: rs863224285) “With Likely benign allele”, ClinVar (classified as likely benign by Invitae, Ambry Genetics and GeneDx, and uncertain significance by Laboratory Corporation of America), Clinvitae (2x), UMD-LSDB (1x as UV), and in control databases in 1 of 245394 chromosomes at a frequency of 0.000004 (Genome Aggregation Database Feb 27, 2017). It was observed in the European Non-Finnish population in 1 of 111050 chromosomes (freq: 0.000009), but not in African, Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The p.Lys1768= variant is not expected to have clinical significance because it does not result in a change of amino acid and occurs outside of the splicing consensus sequence. However, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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