Total submissions: 6
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Invitae | RCV000469918 | SCV000548212 | likely benign | Hereditary nonpolyposis colorectal neoplasms | 2023-12-08 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000481613 | SCV000567440 | uncertain significance | not provided | 2023-10-12 | criteria provided, single submitter | clinical testing | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 18822302, 21120944, 16341550) |
Ambry Genetics | RCV000491178 | SCV000580600 | likely benign | Hereditary cancer-predisposing syndrome | 2023-12-18 | 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. |
Color Diagnostics, |
RCV000491178 | SCV001736387 | uncertain significance | Hereditary cancer-predisposing syndrome | 2022-07-12 | criteria provided, single submitter | clinical testing | This missense variant replaces isoleucine with valine at codon 708 of the MSH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). This variant has been reported in an individual with Lynch syndrome (PMID: 16341550). This variant has been identified in 1/251474 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. |
Prevention |
RCV004533186 | SCV004714467 | uncertain significance | MSH2-related disorder | 2023-12-21 | criteria provided, single submitter | clinical testing | The MSH2 c.2122A>G variant is predicted to result in the amino acid substitution p.Ile708Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. It has conflicting interpretations of likely benign and uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/408499/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. |
All of Us Research Program, |
RCV004000781 | SCV004827862 | uncertain significance | Lynch syndrome | 2023-12-01 | criteria provided, single submitter | clinical testing | This missense variant replaces isoleucine with valine at codon 708 of the MSH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). This variant has been reported in an individual with Lynch syndrome (PMID: 16341550). This variant has been identified in 1/251474 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. |