Total submissions: 12
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clin |
RCV003328173 | SCV000864612 | benign | CDH1-related diffuse gastric and lobular breast cancer syndrome | 2023-08-10 | reviewed by expert panel | curation | The c.188G>A (p.Arg63Gln) variant has an allele frequency of 0.00109 (0.11%, 6/5486 alleles) in the Other subpopulation of the gnomAD cohort (BS1). This variant has also been observed in >10 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, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS1, BS2. |
Gene |
RCV000679566 | SCV000149757 | likely benign | not provided | 2020-12-08 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV000115848 | SCV000185341 | benign | Hereditary cancer-predisposing syndrome | 2018-05-18 | criteria provided, single submitter | clinical testing | This alteration is classified as 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. |
Labcorp Genetics |
RCV000226241 | SCV000288450 | benign | Hereditary diffuse gastric adenocarcinoma | 2025-01-19 | criteria provided, single submitter | clinical testing | |
Color Diagnostics, |
RCV000115848 | SCV000910840 | likely benign | Hereditary cancer-predisposing syndrome | 2015-09-09 | criteria provided, single submitter | clinical testing | |
Institute for Clinical Genetics, |
RCV000679566 | SCV002009860 | uncertain significance | not provided | 2021-11-03 | criteria provided, single submitter | clinical testing | |
Genetic Services Laboratory, |
RCV001796964 | SCV002071976 | likely benign | not specified | 2021-11-23 | criteria provided, single submitter | clinical testing | |
Sema4, |
RCV000115848 | SCV002529099 | benign | Hereditary cancer-predisposing syndrome | 2021-09-18 | criteria provided, single submitter | curation | |
Institute of Human Genetics, |
RCV000226241 | SCV003921059 | likely benign | Hereditary diffuse gastric adenocarcinoma | 2023-02-22 | criteria provided, single submitter | clinical testing | _x000D_ Criteria applied: BS1, BP4 |
Myriad Genetics, |
RCV000226241 | SCV005404177 | likely benign | Hereditary diffuse gastric adenocarcinoma | 2024-09-12 | criteria provided, single submitter | clinical testing | This variant is considered likely benign. Homozygosity has been confirmed in one or more individuals. As homozygosity for pathogenic variants in this gene is generally assumed to result in embryonic lethality, this variant is unlikely to be pathogenic. |
Prevention |
RCV003891615 | SCV000806647 | likely benign | CDH1-related disorder | 2021-02-23 | no assertion criteria provided | 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, |
RCV000226241 | SCV001553806 | uncertain significance | Hereditary diffuse gastric adenocarcinoma | no assertion criteria provided | clinical testing | The CDH1 p.Arg63Gln variant was not identified in the literature nor was it identified in the Cosmic, MutDB, or in the Zhejiang University database. The variant was identified in dbSNP (ID: rs587780117) as "With Uncertain significance allele", and in ClinVar (classified as uncertain significance by GeneDx, Ambry Geneitcs, Invitae). The variant was identified in control databases in 17 of 246200 chromosomes at a frequency of 0.00007 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 15304 chromosomes (freq: 0.00007), Other in 6 of 5486 chromosomes (freq: 0.001), European in 3 of 111650 chromosomes (freq: 0.00003), and South Asian in 7 of 30782 chromosomes (freq: 0.0002); it was not observed in the Latino, Ashkenazi Jewish, East Asian, and Finnish populations. The p.Arg63 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 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. This variant is classified as a variant of uncertain significance. |