22-28709998-ATACT-A

Position:

• chr22-28709998-ATACT-A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_Moderate PP5_Very_Strong

The NM_007194.4(CHEK2):​c.846+4_846+7del variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0000287 in 1,428,834 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000030 (0 hom.)
• Consequence: CHEK2 NM_007194.4 splice_donor_5th_base, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:21 U:1
• Conservation: PhyloP100: 5.62

Genes affected

CHEK2 (HGNC:16627): (checkpoint kinase 2) In response to DNA damage and replication blocks, cell cycle progression is halted through the control of critical cell cycle regulators. The protein encoded by this gene is a cell cycle checkpoint regulator and putative tumor suppressor. It contains a forkhead-associated protein interaction domain essential for activation in response to DNA damage and is rapidly phosphorylated in response to replication blocks and DNA damage. When activated, the encoded protein is known to inhibit CDC25C phosphatase, preventing entry into mitosis, and has been shown to stabilize the tumor suppressor protein p53, leading to cell cycle arrest in G1. In addition, this protein interacts with and phosphorylates BRCA1, allowing BRCA1 to restore survival after DNA damage. Mutations in this gene have been linked with Li-Fraumeni syndrome, a highly penetrant familial cancer phenotype usually associated with inherited mutations in TP53. Also, mutations in this gene are thought to confer a predisposition to sarcomas, breast cancer, and brain tumors. This nuclear protein is a member of the CDS1 subfamily of serine/threonine protein kinases. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 22-28709998-ATACT-A is Pathogenic according to our data. Variant chr22-28709998-ATACT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 216652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.846+4_846+7del		splice_donor_5th_base_variant, intron_variant		ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.846+4_846+7del		splice_donor_5th_base_variant, intron_variant		1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152238 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.0000284 AC: 7 AN: 246676 Hom.: 0 AF XY: 0.0000225 AC XY: 3 AN XY: 133464

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000332

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000541

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000298 AC: 38 AN: 1276596 Hom.: 0 AF XY: 0.0000310 AC XY: 20 AN XY: 644436

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000453

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000517

Gnomad4 SAS exome AF: 0.0000122

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000338

Gnomad4 OTH exome AF: 0.0000186

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152238 Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3 AN XY: 74386

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.000478

Bravo AF: 0.0000604

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:21 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2022	CHEK2: PM2, PS3:Moderate, PP1, PP3 -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 26, 2022	The CHEK2 c.846+4_846+7del variant (rs764884641) is reported in the literature in individuals and families affected with breast cancer (Desrichard 2011, Kleiblova 2019, Mersch 2018). Some individuals carrying this variant are unaffected, suggesting reduced penetrance, and others also carry pathogenic variants in other cancer-associated genes (Kleiblova 2019). This variant is reported in ClinVar (Variation ID: 216652), and is only observed on eight alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant deletes four nucleotides in intron 7, and computational analyses (Alamut v.1.5.1) predict that this variant may impact splicing by significantly weakening the nearby canonical donor splice site. Functional analyses demonstrate skipping of exon 7 or both exons 7 and 8, and also a significant decrease in kinase activity (Casadei 2019, Kleiblova 2019). Based on available information, this variant is considered to be likely pathogenic. References: Casadei S et al. Characterization of splice-altering mutations in inherited predisposition to cancer. Proc Natl Acad Sci U S A. 2019 Dec 16;116(52):26798–807. PMID: 31843900. Desrichard A et al. CHEK2 contribution to hereditary breast cancer in non-BRCA families. Breast Cancer Res. 2011;13(6):R119. PMID: 22114986. Kleiblova P et al. Identification of deleterious germline CHEK2 mutations and their association with breast and ovarian cancer. Int J Cancer. 2019 Oct 1;145(7):1782-1797. PMID: 31050813. Mersch J et al. Prevalence of Variant Reclassification Following Hereditary Cancer Genetic Testing. JAMA. 2018 Sep 25;320(12):1266-1274. PMID: 30264118. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 16, 2023	In the published literature, this variant has been reported in individuals with breast cancer (PMID: 35155181 (2021), 33050356 (2020), 31050813 (2019), 30264118 (2018), 22114986 (2011)). Functional studies demonstrate abnormal splicing and loss of CHEK2 protein kinase function (PMID: 31843900 (2019), 31050813 (2019), 30264118 (2018)). The frequency of this variant in the general population, 0.000099 (5/50340 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper CHEK2 mRNA splicing . Based on the available information, this variant is classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 14, 2023	Observed in multiple individuals with breast cancer, segregating with disease in several families, but two families additionally carried pathogenic variants in other breast cancer susceptibility genes (PMID: 22114986, 31050813, 30264118, 37453313); In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31843900, 22114986, 27485037, 32906215, 25186627, 31422574, 33050356, 32091409, 35155181, 31050813, 30264118, 37725924, 36260514, 37453313, 34326862) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -

Familial cancer of breast Pathogenic:6

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 30, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change falls in intron 7 of the CHEK2 gene. It does not directly change the encoded amino acid sequence of the CHEK2 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs764884641, gnomAD 0.005%). This variant has been observed in individual(s) with hereditary breast cancer (PMID: 22114986, 32906215; Invitae). This variant is also known as c.846+4delAGTA. ClinVar contains an entry for this variant (Variation ID: 216652). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of either exon 7 (in-frame) or exons 7-8 (out-of-frame) (PMID: 30264118; Invitae). The resulting mRNA is expected to either preserve the integrity of the reading frame or undergo nonsense-mediated decay. This variant disrupts the serine/threonine kinase domain of the CHEK2 protein, which is essential for protein function (PMID: 30264118, 31843900, 29785007). While functional studies have not been performed to directly test the effect of this variant on CHEK2 protein function, this suggests that disruption of this region of the protein is causative of disease. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Feb 26, 2024	Criteria applied: PS3_MOD,PS4_MOD,PM2_SUP,PP3 -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	May 18, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jun 27, 2023	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad Internal Data]. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. -
Likely pathogenic, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Aug 26, 2022	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Jan 24, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 17, 2023	This variant deletes 4 nucleotides at the +4 to +7 position of intron 7 of the CHEK2 gene. Functional RNA studies have shown that this variant produces two mutant transcripts (PMID: 31050813, 31843900). One mutant transcript causes an out-of-frame skipping of exons 7 and 8, creating a frameshift and premature translation stop signal and is expected to result in an absent or non-functional protein product. The other mutant transcript causes an in-frame skipping of exon 7, creating a partial deletion of the kinase domain. A functional study has shown that a variant lacking exon 7 displays significantly decreased kinase activity (PMID: 31050813). This variant has been reported in more than ten individuals affected with familial breast cancer (PMID: 22114986, 30264118, 31050813; Color internal data). This variant has also been identified in 8/278088 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 Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 03, 2023	The c.846+4_846+7delAGTA intronic variant is located 4 nucleotides after coding exon 6 of the CHEK2 gene and results from a deletion of 4 nucleotides at positions c.846+4 to c.846+7. In one study, c.846+4_846+7delAGTA was detected in a French woman with breast cancer who previously tested negative for mutations in the BRCA1 and BRCA2 genes (Desrichard A et al. Breast Cancer Res. 2011;13:R119). This nucleotide region is well 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 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 variant is likely to be pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Dec 10, 2020	The c.846+4_846+7del variant in intron 7 of the CHEK2 gene has been reported in more than 10 individuals affected with breast cancer (PMID: 22114986, 30264118, 31050813). It was shown to produce two mutant transcripts in an RNA study (PMID: 31050813). One mutant transcript results in out-of-frame skipping of exons 7 and 8, creating a frameshift and a premature translation stop signal expected to result in an absent or non-functional protein product. The other mutant transcript results in an in-frame skipping of exon 7, creating a partial deletion of the kinase domain and significantly decreased kinase activity (PMID: 31050813). This variant has been identified in 8/278088 alleles in the gnomAD population database. Therefore, the c.846+4_846+7del variant in the CHEK2 gene is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 02, 2024	Variant summary: CHEK2 c.846+4_846+7delAGTA alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing leading to two populations of transcript, one causing the complete in-frame skipping of exon 7 and another leading to an out of frame skipping of exons 7 and 8 (Casadei_2019). The variant allele was found at a frequency of 2.8e-05 in 246676 control chromosomes. c.846+4_846+7delAGTA has been reported in the literature in settings of multigene panel testing and focused CHEK2 screening among individuals with a personal and family history of breast and other cancers (example, Desrichard_2011, Tung_2015, Kleibova_2019, Vargas-Parra_2020, Stolarova_2020, Barbalho_2020) and in at-least once in a cohort of individuals without a cancer diagnosis (example, Kraemer_2019). However, it has also been reported as a VUS in settings of multigene panel testing in an individual with male breast cancer (Tung_2015), as a VUS when classified based on the framework of Senol-Cosar_2019 for low penetrant genes (Vargas-Parra_2020). Several instances of unaffected family members harboring this variant have also been reported (Kleibova_2019). These data indicate that the variant is likely to be associated with disease with a variable penetrance. At-least three instances of co-occurrences with other putative pathogenic variant(s) have been reported (ATM, p.R2034Cfs*; BRCA2, p.N433Qfs*; BRCA2, p.C1200*), providing supporting evidence for a benign/non-actionable role (Kleibova_2019). At least one publication reports experimental evidence evaluating an impact on protein function (Kleibova_2019). The most pronounced variant effect results in a significantly diminished CHEK2 kinase activity in vitro in an experimental system that measured relative levels of CHK2-dependent KAP1-S473 phosphorylation in RPE1-CHEK2-KO cells. The following publications have been ascertained in the context of this evaluation (PMID: 25186627, 22114986, 31422574, 31050813, 32906215, 31843900, 33050356, 35155181). ClinVar contains an entry for this variant (Variation ID: 216652). Based on the evidence outlined above, the variant was classified as pathogenic. -

Li-Fraumeni syndrome 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Jan 25, 2024

PS3, PS4_Moderate -

Carcinoma of pancreas Pathogenic:1

Pathogenic, no assertion criteria provided

case-control

CZECANCA consortium

Mar 04, 2021

- -

Familial cancer of breast;C5882668:Li-Fraumeni syndrome 2 Pathogenic:1

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

Endometrial carcinoma Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

CZECANCA consortium

Feb 21, 2023

- -

not specified Uncertain:1

Uncertain significance, flagged submission

clinical testing

Genetic Services Laboratory, University of Chicago

Aug 12, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.98		Position offset: 8

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs764884641; hg19: chr22-29105986;