ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.2073C>T (p.Ala691=)

gnomAD frequency: 0.00001  dbSNP: rs536104508
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162447 SCV000212800 likely benign Hereditary cancer-predisposing syndrome 2015-07-01 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.
GeneDx RCV000757065 SCV000723574 likely benign not provided 2019-07-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24204729)
Labcorp Genetics (formerly Invitae), Labcorp RCV001088659 SCV000760883 likely benign Hereditary diffuse gastric adenocarcinoma 2023-11-15 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000757065 SCV000885154 likely benign not provided 2017-12-18 criteria provided, single submitter clinical testing The CDH1 c.2073C>T; p.Ala691Ala variant is listed in the medical literature in an individual with gastric cancer (Garziera 2013). However, the variant is also listed as likely benign in the ClinVar database (Variation ID: 183737). The variant is listed in the dbSNP variant database (rs536104508) and in the Genome Aggregation Database in 3/277160 alleles. This is a silent variant, the nucleotide at this position is not conserved, and computational algorithms (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict no significant change in splicing. Considering available information, this variant is classified as likely benign. References: Garziera M et al. Identification and characterization of CDH1 germline variants in sporadic gastric cancer patients and in individuals at risk of gastric cancer. PLoS One. 2013 Oct 29;8(10):e77035.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000602744 SCV000919117 likely benign not specified 2019-08-28 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000162447 SCV001354015 likely benign Hereditary cancer-predisposing syndrome 2019-05-02 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV001088659 SCV005402835 benign Hereditary diffuse gastric adenocarcinoma 2024-09-20 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.
True Health Diagnostics RCV000162447 SCV000787980 likely benign Hereditary cancer-predisposing syndrome 2018-02-20 no assertion criteria provided clinical testing

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