ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1500C>T (p.Gly500=)

gnomAD frequency: 0.00001  dbSNP: rs781317341
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen CDH1 Variant Curation Expert Panel RCV003993842 SCV004812912 likely benign CDH1-related diffuse gastric and lobular breast cancer syndrome 2023-08-28 reviewed by expert panel curation The NM_004360.5:c.1500C>T (p.Gly500=) variant results in a synonymous amino acid variant within exon 10. This variant is present at an allele frequency of 0.00002828 (8/282862) in gnomAD v2.1.1, with a maximum frequency of 0.0003508 (7/19954) in the East Asian subpopulation. The variant has been observed in more than 10 (97) individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2). This variant occurs at a nucleotide that is not predicted to alter splicing or protein function by multiple in silico predictors (BP7, BP4). In summary, this variant meets criteria to be classified as likely benign based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2, BP4, BP7.
Ambry Genetics RCV000162599 SCV000213019 likely benign Hereditary cancer-predisposing syndrome 2014-10-30 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.
Counsyl RCV000411626 SCV000489219 likely benign Hereditary diffuse gastric adenocarcinoma 2016-09-09 criteria provided, single submitter clinical testing
GeneDx RCV000731865 SCV000515793 likely benign not provided 2019-09-17 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 27616075)
Labcorp Genetics (formerly Invitae), Labcorp RCV000411626 SCV000557424 likely benign Hereditary diffuse gastric adenocarcinoma 2023-12-29 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000162599 SCV000684362 likely benign Hereditary cancer-predisposing syndrome 2016-12-23 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000731865 SCV000859721 uncertain significance not provided 2018-02-27 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000731865 SCV001245992 uncertain significance not provided 2019-11-01 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000162599 SCV002529069 benign Hereditary cancer-predisposing syndrome 2020-11-29 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV000411626 SCV004019998 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.
True Health Diagnostics RCV000162599 SCV000787976 likely benign Hereditary cancer-predisposing syndrome 2017-10-10 no assertion criteria provided clinical testing

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