ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.688-4T>C

gnomAD frequency: 0.00003  dbSNP: rs781633588
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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 RCV000218860 SCV000273711 likely benign Hereditary cancer-predisposing syndrome 2019-05-16 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other data supporting benign classification
GeneDx RCV000425352 SCV000512509 likely benign not specified 2017-09-08 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 RCV000218860 SCV000911792 likely benign Hereditary cancer-predisposing syndrome 2016-04-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000425352 SCV000919096 uncertain significance not specified 2017-09-19 criteria provided, single submitter clinical testing Variant summary: The CDH1 c.688-4T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was found in the control population dataset of gnomAD in 2/246212 control chromosomes at a frequency of 0.0000081, which does not exceed the estimated maximal expected allele frequency of a pathogenic CDH1 variant (0.0000283). The variant has been reported in the literature, without strong evidence for causality (Yorczyk_2015). One clinical diagnostic laboratory classified this variant as uncertain significance and one as likely benign. Taken together, this variant is classified as VUS.
Invitae RCV000875193 SCV001017484 likely benign Hereditary diffuse gastric adenocarcinoma 2021-03-29 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000425352 SCV002070061 likely benign not specified 2019-12-31 criteria provided, single submitter clinical testing

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