ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1239C>T (p.Tyr413=)

gnomAD frequency: 0.00041  dbSNP: rs36074916
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163580 SCV000214139 likely benign Hereditary cancer-predisposing syndrome 2014-07-29 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000197325 SCV000252789 benign Hereditary diffuse gastric adenocarcinoma 2024-01-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000244292 SCV000310122 benign not specified criteria provided, single submitter clinical testing
Counsyl RCV000197325 SCV000488639 likely benign Hereditary diffuse gastric adenocarcinoma 2016-05-12 criteria provided, single submitter clinical testing
GeneDx RCV000244292 SCV000518176 benign not specified 2015-08-03 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 Diagnostics, LLC DBA Color Health RCV000163580 SCV000684344 likely benign Hereditary cancer-predisposing syndrome 2015-10-01 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759724 SCV000889242 benign not provided 2023-01-16 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000244292 SCV000917115 benign not specified 2017-10-31 criteria provided, single submitter clinical testing Variant summary: The CDH1 c.1239C>T (p.Tyr413Tyr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in 37/277230 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001207 (29/24032). This frequency is about 43 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 African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign or likely benign. Taken together, this variant is classified as benign.
Sema4, Sema4 RCV000163580 SCV002531153 benign Hereditary cancer-predisposing syndrome 2021-07-30 criteria provided, single submitter curation
European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto RCV000197325 SCV003926758 likely benign Hereditary diffuse gastric adenocarcinoma 2022-08-01 criteria provided, single submitter clinical testing BS1 (PMID: 30311375)
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003316002 SCV004017025 benign Malignant tumor of prostate 2023-07-07 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000197325 SCV004019993 benign Hereditary diffuse gastric adenocarcinoma 2023-03-06 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.
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000163580 SCV005045341 benign Hereditary cancer-predisposing syndrome 2024-01-23 criteria provided, single submitter clinical testing

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