ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1684A>G (p.Thr562Ala)

gnomAD frequency: 0.00002  dbSNP: rs587782061
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen CDH1 Variant Curation Expert Panel RCV003328216 SCV004035103 likely benign CDH1-related diffuse gastric and lobular breast cancer syndrome 2023-08-03 reviewed by expert panel curation The NM_004360.5(CDH1):c.1684A>G (p.Thr562Ala) variant has been observed in >10 individuals without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; internal laboratory contributors). In summary, the clinical significance of this variant is classified as likely benign based on BS2 alone. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel: BS2. (CDH1 VCEP specifications version 3.1; 06/26/2023)
Ambry Genetics RCV000130539 SCV000185408 likely benign Hereditary cancer-predisposing syndrome 2019-03-25 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 RCV000233909 SCV000288444 likely benign Hereditary diffuse gastric adenocarcinoma 2024-01-27 criteria provided, single submitter clinical testing
Counsyl RCV000233909 SCV000488384 uncertain significance Hereditary diffuse gastric adenocarcinoma 2016-03-11 criteria provided, single submitter clinical testing
GeneDx RCV001283957 SCV000517007 likely benign not provided 2018-11-28 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000130539 SCV000689476 likely benign Hereditary cancer-predisposing syndrome 2017-05-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001283957 SCV001469486 uncertain significance not provided 2020-06-26 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000130539 SCV002529084 likely benign Hereditary cancer-predisposing syndrome 2021-06-28 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV000233909 SCV004019593 uncertain significance Hereditary diffuse gastric adenocarcinoma 2023-03-06 criteria provided, single submitter clinical testing This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.
PreventionGenetics, part of Exact Sciences RCV003390820 SCV004119104 uncertain significance CDH1-related disorder 2023-05-30 criteria provided, single submitter clinical testing The CDH1 c.1684A>G variant is predicted to result in the amino acid substitution p.Thr562Ala. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0062% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-68853301-A-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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