ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1020G>A (p.Thr340=)

gnomAD frequency: 0.00008  dbSNP: rs61747632
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212360 SCV000210881 benign not specified 2014-08-01 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.
Ambry Genetics RCV000160372 SCV000213321 likely benign Hereditary cancer-predisposing syndrome 2014-09-09 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
Invitae RCV000198410 SCV000252787 benign Hereditary diffuse gastric adenocarcinoma 2021-12-08 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000198410 SCV000398559 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Color Diagnostics, LLC DBA Color Health RCV000160372 SCV000684325 likely benign Hereditary cancer-predisposing syndrome 2015-04-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588315 SCV000698352 benign not provided 2016-08-08 criteria provided, single submitter clinical testing Variant summary: The CDH1 c.1020G>A (p.Thr340Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this variant while splice prediction tools indicate the variant not to have an impact on normal splicing. This variant was found in 22/121410 control chromosomes (1 homozygote), predominantly observed in the East Asian subpopulation at a frequency of 0.00104 (9/8654). This frequency is about 37 times the estimated maximal expected allele frequency of a pathogenic CDH1 variant (0.0000283), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Counsyl RCV000198410 SCV000786161 likely benign Hereditary diffuse gastric adenocarcinoma 2018-03-12 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588315 SCV000889234 benign not provided 2017-11-13 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV001798549 SCV002043247 likely benign Breast and/or ovarian cancer 2020-04-30 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000212360 SCV002067078 likely benign not specified 2021-01-07 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000160372 SCV002531136 benign Hereditary cancer-predisposing syndrome 2021-10-11 criteria provided, single submitter curation
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000588315 SCV001957952 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000588315 SCV001966084 likely benign not provided no assertion criteria provided clinical testing

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