ClinVar Genomic variation as it relates to human health

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Observed in individuals with CHEK2-related cancers (Mantere 2017, Rohlin 2017, Brovkina 2018, Dominguez-Valentin 2018, Olkinuora 2018); Case control studies, in the Finnish population, suggest this variant is associated with breast cancer (Nurmi 2019); Not observed at a significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 31948886, 31882575, 30927251, 30333958, 30573798, 27751358, 27696107, 28386063, 24713400, 28608266, 26681312, 23960188)

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

This sequence change affects a donor splice site in intron 2 of the CHEK2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and is likely to result in the loss of the initiator methionine. This variant is present in population databases (rs587782401, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with thyroid cancer, colorectal cancer, prostate cancer, and breast and/or ovarian cancer (PMID: 26681312, 27696107, 28608266, 30333958, 30927251, 31882575, 31948886). ClinVar contains an entry for this variant (Variation ID: 142352). Studies have shown that disruption of this splice site results in skipping of exon 2, and is expected to result in the loss of the initiator methionine (Invitae). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

The c.319+2T>A pathogenic intronic mutation results from a T to A substitution two nucleotides after coding exon 1 in the CHEK2 gene. The alteration has previously been reported in an individual diagnosed with a microsatellite-stable colorectal cancer at age 76 years (Rohlin A et al. Fam. Cancer 2017 Apr;16(2):195-203) and in another individual diagnosed with thyroid cancer and bilateral breast cancer who also had a family history of breast, thyroid, and endometrial cancers (Dominguez-Valentin M et al. Fam. Cancer 2018 Jan;17(1):141-153).This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this alteration is interpreted as a disease-causing mutation.

This c.319+2T>A variant in CHEK2 gene affects 5’ splice site of intron 2. The variant is expected to disrupt normal splicing of CHEK2 mRNA, leading to an absent or abnormal protein product. This variant has been reported in multiple unrelated individuals with breast, colorectal and thyroid cancers (PMID: 28386063, 27696107, 28608266). It is present in 29/282228 alleles in the gnomAD population database. Based on the currently available information, the CHEK2 c.319+2T>A variant has been classified as likely pathogenic.

This variant disrupts a canonical splice-donor site and interferes with normal CHEK2 mRNA splicing. In the published literature, the variant has been reported in individuals with breast and/or ovarian cancer(PMIDs: 31882575 (2019), 30333958 (2018), 28608266 (2017), 26681312 (2015)), and in an individual with colorectal cancer (PMID: 27696107 (2016)). Based on the available information, this variant is classified as likely pathogenic.

Variant summary: CHEK2 c.319+2T>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 5' splicing donor site. A recent report confirmed this prediction, by demonstrating that the variant didn't produce any full length transcripts in a splicing reporter minigene assay (Sanoguera-Miralles_2023). The variant allele was found at a frequency of 0.0001 in 282,228 control chromosomes (gnomAD v2.1), however in some subpopulations e.g. in the Finnish and Estonian the variant was reported with much higher frequencies, i.e. 0.0006 and 0.0019 respectively. These subpopulation frequencies are higher than the estimated maximum expected for a pathogenic variant in CHEK2 causing Breast Cancer phenotype (0.00031). The variant has been reported in patients with breast cancer and other tumor phenotypes, including e.g. microsatellite-stable colorectal cancer and Cowden-like syndrome (e.g. de Miranda_2013, Susswein_2015, Leedom_2016, Rohlin_2016, Dominguez-Valentin_2017). In a large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 20/60,466 cases, and 7/53,461 controls (Dorling_2021, reported through LOVD). A case control study in the Finnish population, suggested that this variant is associated with elevated risk of breast cancer (Nurmi_2022). While another case-control study performed in Estonians showed that the relative frequency of the variant in the in the general population is 0.09%, and in variant carriers most breast cancer cases were diagnosed after the age of 50y (Pavlovica_2022). The following publications have been ascertained in the context of this evaluation (PMID: 23960188, 26681312, 27696107, 28608266, 27751358, 33471991, 35314380, 36551643, 37725924). 13 other submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic (n=3) or likely pathogenic (n=10). Based on the evidence outlined above, the variant was classified as pathogenic.

This variant causes a T>A nucleotide substitution at the +2 position of intron 2 of the CHEK2 gene. Computational splicing tools predict that this variant may have a significant impact on RNA splicing. To our knowledge, functional RNA studies have not been reported for this variant. This variant has been reported in individuals affected with breast cancer and ovarian cancer (PMID: 26681312, 28608266, 30333958, 31882575) and in an individual who was referred for clinical familial adenomatous polyposis- and/or Lynch syndrome mutation analyses (PMID: 27696107). In the Finnish population where this variant has been identified in 15/25102 chromosomes, this variant is associated with elevated risk of breast cancer (PMID: 30927251). This variant has been identified in 29/282228 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of CHEK2 function is a known mechanism of disease. Based on available evidence, this variant is classified as Likely Pathogenic.