ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1689C>T (p.Ala563=)

gnomAD frequency: 0.00003  dbSNP: rs587780786
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000123240 SCV000166546 likely benign Hereditary diffuse gastric adenocarcinoma 2024-01-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162614 SCV000213045 likely benign Hereditary cancer-predisposing syndrome 2015-01-20 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Illumina Laboratory Services, Illumina RCV000123240 SCV000398567 likely benign Hereditary diffuse gastric adenocarcinoma 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000433853 SCV000512524 benign not specified 2015-04-27 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 RCV001281702 SCV000600964 likely benign not provided 2019-09-16 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000162614 SCV000684376 likely benign Hereditary cancer-predisposing syndrome 2017-05-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000433853 SCV001338306 likely benign not specified 2020-02-15 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000123240 SCV005404162 benign Hereditary diffuse gastric adenocarcinoma 2024-09-19 criteria provided, single submitter clinical testing This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.
PreventionGenetics, part of Exact Sciences RCV003935175 SCV004764382 likely benign CDH1-related disorder 2019-10-07 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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