Total submissions: 9
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Gene |
RCV000235646 | SCV000292935 | uncertain significance | not provided | 2019-04-18 | criteria provided, single submitter | clinical testing | Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 22949387, 22290698, 18383312, 16995940, 26333163, 26951660, 14526391) |
Ambry Genetics | RCV000491084 | SCV000580531 | likely benign | Hereditary cancer-predisposing syndrome | 2022-09-29 | 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. |
Invitae | RCV000630103 | SCV000751059 | benign | Hereditary nonpolyposis colorectal neoplasms | 2023-12-30 | criteria provided, single submitter | clinical testing | |
Sema4, |
RCV000491084 | SCV002534559 | uncertain significance | Hereditary cancer-predisposing syndrome | 2021-08-23 | criteria provided, single submitter | curation | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV002265598 | SCV002547922 | uncertain significance | not specified | 2022-05-23 | criteria provided, single submitter | clinical testing | Variant summary: MSH2 c.742A>G (p.Lys248Glu) results in a conservative amino acid change located in the DNA mismatch repair protein MutS, connector domain (IPR007860) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251368 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. Although reported in the literature (example, Lastella_2006), to our knowledge, no case level occurrence of c.742A>G in individuals affected with Lynch Syndrome has been reported. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect although reporting a consensus classification of neutral (example, Jia_2021). Therefore, this study is not weighted as a directly traceable evidence in the context of this evaluation. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. |
Baylor Genetics | RCV003389041 | SCV004194501 | uncertain significance | Lynch syndrome 1 | 2023-07-27 | criteria provided, single submitter | clinical testing | |
Color Diagnostics, |
RCV000491084 | SCV004356627 | uncertain significance | Hereditary cancer-predisposing syndrome | 2023-11-15 | criteria provided, single submitter | clinical testing | This missense variant replaces lysine with glutamic acid at codon 248 of the MSH2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, 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). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 5/251368 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. |
All of Us Research Program, |
RCV003997180 | SCV004821672 | uncertain significance | Lynch syndrome | 2024-02-05 | criteria provided, single submitter | clinical testing | This missense variant replaces lysine with glutamic acid at codon 248 of the MSH2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, 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). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 5/251368 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. |
Zotz- |
RCV003389041 | SCV004101130 | uncertain significance | Lynch syndrome 1 | 2023-11-02 | no assertion criteria provided | clinical testing |