ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.303C>T (p.Tyr101=)

gnomAD frequency: 0.00027  dbSNP: rs150789339
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 17
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162725 SCV000213191 likely benign Hereditary cancer-predisposing syndrome 2014-10-29 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.
Invitae RCV000197624 SCV000253422 benign Hereditary diffuse gastric adenocarcinoma 2024-01-25 criteria provided, single submitter clinical testing
Counsyl RCV000197624 SCV000488620 likely benign Hereditary diffuse gastric adenocarcinoma 2016-05-10 criteria provided, single submitter clinical testing
GeneDx RCV000441897 SCV000512505 benign not specified 2015-08-27 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.
Color Diagnostics, LLC DBA Color Health RCV000162725 SCV000684452 likely benign Hereditary cancer-predisposing syndrome 2015-12-30 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001800474 SCV001471954 likely benign not provided 2020-01-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000441897 SCV002041675 benign not specified 2021-11-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000441897 SCV002047317 benign not specified 2021-02-04 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000162725 SCV002529167 likely benign Hereditary cancer-predisposing syndrome 2021-08-04 criteria provided, single submitter curation
Fulgent Genetics, Fulgent Genetics RCV002498805 SCV002804677 likely benign Familial cancer of breast; Blepharocheilodontic syndrome 1; Endometrial carcinoma; Hereditary diffuse gastric adenocarcinoma; Neoplasm of ovary; Malignant tumor of prostate 2021-10-27 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario RCV003149992 SCV003837761 likely benign Breast and/or ovarian cancer 2021-06-24 criteria provided, single submitter clinical testing
European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto RCV000197624 SCV003927015 uncertain significance Hereditary diffuse gastric adenocarcinoma 2022-08-01 criteria provided, single submitter clinical testing BP7 (PMID: 30311375)
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003315982 SCV004017013 benign Malignant tumor of prostate 2023-07-07 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000197624 SCV004019984 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.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000441897 SCV004026628 likely benign not specified 2023-08-15 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003917558 SCV004744894 likely benign CDH1-related disorder 2019-04-24 criteria provided, single submitter 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).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000197624 SCV001552497 likely benign Hereditary diffuse gastric adenocarcinoma no assertion criteria provided clinical testing The CDH1 p.Tyr101= variant was not identified in the literature. The variant was identified in dbSNP (ID: rs150789339) as "With Likely benign allele" and ClinVar (classified as benign by GeneDx; and as likely benign by Invitae, Ambry Genetics, Counsyl and Color). The variant was identified in control databases in 21 of 276986 chromosomes at a frequency of 0.00008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 16 of 24034 chromosomes (freq: 0.0007), Other in 1 of 6460 chromosomes (freq: 0.0002), Latino in 2 of 34416 chromosomes (freq: 0.000068), and European in 2 of 126494 chromosomes (freq: 0.00002), while the variant was not observed in the Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. The p.Tyr101= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.