ClinVar Miner

Submissions for variant NM_007194.4(CHEK2):c.1260-10C>G

gnomAD frequency: 0.00006  dbSNP: rs730881706
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000160459 SCV000211024 benign not specified 2014-08-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000199374 SCV000253480 likely benign Familial cancer of breast 2021-12-15 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000581114 SCV000684577 benign Hereditary cancer-predisposing syndrome 2017-03-20 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000160459 SCV000917228 benign not specified 2017-09-07 criteria provided, single submitter clinical testing Variant summary: The CHEK2 c.1260-10C>G variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 6/110696 control chromosomes (1 homozygote) in ExAC and 17/275124 control chromosomes in gnomAD (1 homozygote), predominantly observed in the European (Non-Finnish) subpopulation at frequency of 0.0001 (6/59812 in ExAC) and 0.0001355 (17/125452 in genomAD). These frequency are about 4 ~ 5 times the estimated maximal expected allele frequency of a pathogenic CHEK2 variant (0.0000284), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. This variant has been reported in one BrC patient without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Genetic Services Laboratory,University of Chicago RCV000160459 SCV002066144 likely benign not specified 2020-09-08 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000581114 SCV002537037 likely benign Hereditary cancer-predisposing syndrome 2021-03-24 criteria provided, single submitter curation
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV001528944 SCV001741561 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV001528944 SCV001905856 likely benign not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV001528944 SCV001956741 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001528944 SCV001980650 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001528944 SCV002036506 likely benign not provided no assertion criteria provided clinical testing

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