ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.833-3C>T

gnomAD frequency: 0.00003  dbSNP: rs587782839
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000132428 SCV000187521 likely benign Hereditary cancer-predisposing syndrome 2020-01-29 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.
GeneDx RCV000478649 SCV000569148 uncertain significance not provided 2016-08-06 criteria provided, single submitter clinical testing This variant is denoted CDH1 c.833-3C>T or IVS6-3C>T and consists of a C>T nucleotide substitution at the -3 position of intron 6 of the CDH1 gene. This variant is not predicted to impact splicing; however, in the absence of RNA or functional studies, the actual effect of this variant is unknown. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. CDH1 c.833-3C>T was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The cytosine (C) nucleotide that is altered is not conserved across species. Based on currently available information, it is unclear whether CDH1 c.833-3C>T is pathogenic or benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV000545148 SCV000637857 likely benign Hereditary diffuse gastric adenocarcinoma 2025-01-05 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000132428 SCV000908727 uncertain significance Hereditary cancer-predisposing syndrome 2024-01-03 criteria provided, single submitter clinical testing This variant causes a C to T nucleotide substitution at the -3 position of intron 6 of the CDH1 gene. Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with CDH1-related disorders in the literature. This variant has been identified in 2/31380 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Sema4, Sema4 RCV000132428 SCV002529216 uncertain significance Hereditary cancer-predisposing syndrome 2021-10-12 criteria provided, single submitter curation
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000478649 SCV004220846 likely benign not provided 2023-05-11 criteria provided, single submitter clinical testing

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