Submissions for variant NM_007194.4(CHEK2):c.1461+2T>C

dbSNP: rs779844113

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000693670	SCV000821548	likely pathogenic	Familial cancer of breast	2023-11-24	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 13 of the CHEK2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CHEK2 are known to be pathogenic (PMID: 21876083, 24713400). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with personal or family history of breast and/or ovarian cancer (PMID: 24549055, 31159747). ClinVar contains an entry for this variant (Variation ID: 572314). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
GeneKor MSA	RCV000708609	SCV000821729	likely pathogenic	not provided	2020-01-01	criteria provided, single submitter	clinical testing	This sequence change occurs 2 nucleotides after exon 13 of the CHEK2 gene. This position is highly conserved in the human and other genomes and is crucial in mRNA processing. This variant is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Truncating variants in CHEK2 are known to be pathogenic (PMID: 21876083, 24713400). Also, donor and acceptor splice site variants as usual lead to a loss of protein function (PMID: 16199547). This variant has been described in the international literature in individuals with personal or family history of breast and/or ovarian cancer(PMID:24549055) and an individual undergoing panel testing for hereditary syndrome (PMID: 31159747). The mutation database ClinVar contains entries for this variant (Variation ID:572314).
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000708609	SCV001446735	likely pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002388249	SCV002701953	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-07-29	criteria provided, single submitter	clinical testing	The c.1461+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 12 in the CHEK2 gene. This alteration has been identified in a cohort of high-risk breast/ovarian cancer patients (Castéra L et al. Eur J Hum Genet, 2014 Nov;22:1305-13). This alteration has also been reported in 1/1197 individuals from Greece, Romania, and Turkey undergoing evaluation for inherited cancer predisposition (Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535). 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). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Myriad Genetics, Inc.	RCV000693670	SCV004043574	likely pathogenic	Familial cancer of breast	2023-06-28	criteria provided, single submitter	clinical testing	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.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV003492132	SCV004240448	likely pathogenic	Breast and/or ovarian cancer	2023-05-17	criteria provided, single submitter	clinical testing