rs587782849

Positions:

• chr22-28724974-T-A
• chr22-28724974-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PP3 PP5_Very_Strong

The NM_007194.4(CHEK2):​c.592+3A>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: CHEK2 NM_007194.4 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9976
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:23 U:2
• Conservation: PhyloP100: 3.10

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 Likely_pathogenic. Variant got 9 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, max_spliceai. No scorers claiming Uncertain. Scorers claiming Benign: dbscSNV1_RF.
• PP5: Variant 22-28724974-T-A is Pathogenic according to our data. Variant chr22-28724974-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 142956.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-28724974-T-A is described in Lovd as [Pathogenic]. Variant chr22-28724974-T-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.592+3A>T		splice_donor_region_variant, intron_variant		ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.592+3A>T		splice_donor_region_variant, intron_variant		1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152116 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000318 AC: 8 AN: 251318 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135866

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: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000616

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000151 AC: 22 AN: 1461750 Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12 AN XY: 727188

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000144

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152116 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74320

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000434 Hom.: 0

Bravo AF: 0.0000151

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:23 Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:9

Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 22, 2024	PVS1_strong+PS4_mod+PM2_sup -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 01, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg	Aug 01, 2023	This variant has been identified by standard clinical testing. Selected ACMG criteria: Pathogenic (I):PP5;PS4;PVS1 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 27, 2023	The CHEK2 c.592+3A>T variant has been reported in the published literature in in individuals with breast cancer including early age of onset (PMID: 27616075 (2016), 29522266 (2018), 33925588 (2021), 33919281 (2021), 31300551 (2020)) and colorectal cancer (PMID: 27978560 (2016)). This variant was reported to result in aberrant splicing and the alternative transcripts are predicted to result in truncated CHEK2 protein (PMID: 27616075 (2016), 33925588 (2021)). However, another study analyzing the fraction of transcripts in a patient carrying this variant found that 55% of transcripts were wild type (31843900 (2019)). Hence the effects of this splicing on CHECK2 protein function are inconclusive. The frequency of this variant in the general population, 0.034 (297/8700 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	CHEK2: PM2, PS4:Moderate, PP3, PS3:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 08, 2023	Observed in individuals with CHEK2-related cancers and suggested to be a Greek founder variant (PMID: 27616075, 27978560, 29522266, 32658311, 33925588, 35418818, 35264596); Non-canonical splice site variant demonstrated to result in aberrant splicing leading to a null allele in a gene for which loss of function is a known mechanism of disease (PMID: 27616075, 31843900, 33925588); In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.721+3A>T; This variant is associated with the following publications: (PMID: 27616075, 27978560, 29522266, 32658311, 31843900, 31300551, 34426522, 33925588, 35220195, 35264596, 35418818) -
Likely pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Familial cancer of breast Pathogenic:6 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 27, 2024	- -
Uncertain significance, flagged submission	clinical testing	Counsyl	Jun 27, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	May 18, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 08, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad Internal Data]. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 21, 2024	This sequence change falls in intron 4 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 (rs587782849, gnomAD 0.005%). This variant has been observed in individual(s) with breast cancer and colorectal cancer (PMID: 27616075, 27978560, 29522266, 32658311, 33919281, 33980423). ClinVar contains an entry for this variant (Variation ID: 142956). 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 complex altered splicing including up regulation of naturally occurring isoforms and skipping of exon 4 (also known as exon 3) and skipping of exon 4 and 5, which introduce premature termination codons. The resulting mRNA is expected to undergo nonsense-mediated decay. This variant causes significant reduction of the normal transcript (PMID: 27616075, 31843900, 33925588; 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Mar 30, 2023	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 20, 2023	This variant causes an A>T nucleotide substitution at the +3 position of intron 4 of the CHEK2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies with heterozygous carriers have shown that this variant causes aberrant splicing and causes out-of-frame skipping of exon 4, or exons 4 and 5 (PMID: 27616075, 31843900, 33925588). The observed exon skipping is expected to result in nonsense-mediated decay of the mutant transcripts. An external laboratory has also reported observation of abnormal splicing in multiple carriers based on their internal RNA studies (ClinVar SCV000187541.6). This variant has been reported in over twenty individuals affected with breast cancer (PMID: 27616075, 28486781, 29522266, 31300551, 32658311, 33919281, 33925588, 33980423), colorectal cancer (PMID: 27978560), and prostate cancer (PMID: 35350808). A haplotype analysis has shown a founder effect of this variant for individuals of Greek descent (PMID: 33925588). This variant has also been identified in 8/251318 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of CHEK2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 14, 2023	The c.592+3A>T intronic variant results from an A to T substitution 3 nucleotides after coding exon 3 in the CHEK2 gene. This alteration has been detected in multiple breast cancer cohorts (Hauke J et al. Cancer Med, 2018 04;7:1349-1358;Fostira F et al. J. Med. Genet., 2020 01;57:53-61; Akcay IM et al. Int J Cancer, 2021 Jan;148:285-295; Apostolou P et al. Cancers (Basel), 2021 Apr;13). This alteration was also identified in one patient with colorectal cancer at 39 years of age (Pearlman R et al. JAMA Oncol. 2017 Apr;3:464-471). RNA analysis from a breast cancer patient who carried this variant identified two abnormally spliced transcripts predicted to result nonsense-mediated decay (Kraus C et al. Int. J. Cancer. 2017 Jan;140:95-102), and another RNA study demonstrated this alteration has a deleterious splicing impact (Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec). In addition, internal RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Feb 11, 2022	- -

CHEK2-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 14, 2024

The CHEK2 c.592+3A>T variant is predicted to interfere with splicing. This variant has been reported in individuals with colorectal cancer (Pearlman et al. 2017, eTable 2. PubMed ID: 27978560; Akcay. 2020. PubMed ID: 32658311; Ercoskun and Ozkan. 2022. PubMed ID: 35418818), breast cancer (Table 1, Kraus et al. 2017. PubMed ID: 27616075; reported as c.721+3A>T in Table 3, Bora et al. 2022. PubMed ID: 35220195; Toss et al. 2021. PubMed ID: 33919281; Ece Solmaz et al. 2021. PubMed ID: 33980423), and breast/ovarian cancer (Table S1, Kauke et al. 2018. PubMed ID:29522266). Functional analysis (RT-PCR) has demonstrated the formation of two different shortened CHEK2 transcripts, one lacking exon 4 and the other lacking exons 4-5 (Figure 1, Kraus et al. 2017. PubMed ID: 27616075). This variant is reported in 0.0062% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from uncertain to likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/142956/). In summary, this variant is interpreted as likely pathogenic. -

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

- -

Malignant tumor of breast Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

May 11, 2024

- -

Malignant tumor of prostate Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar

-

- -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Nov 08, 2022

Variant summary: CHEK2 c.592+3A>T 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: Two predict the variant abolishes a canonical 5 prime splicing donor site, while two predict the variant weakens the 5 prime donor site. At least two publications report experimental evidence that this variant affects mRNA splicing, leading to the skipping of exon 4 and exon 4/5, both predicted to cause a frameshift (e.g. Kraus_2016, Casadei_2019). The variant allele was found at a frequency of 3.6e-05 in 252298 control chromosomes (gnomAD and Akcay_2021). c.592+3A>T has been reported in the literature in multiple individuals affected with breast and/or ovarian cancer, some of these cases were diagnosed at an early age and/or indicated to have a positive family history and several patients were comprehensively genotyped on large cancer gene panels (e.g. Kraus_2016, Lolas Hamameh_2017, Hauke_2018, Fostria_2020, Akcay_2021, Toss_2021, Bora_2022). These reports indicate that the variant is likely associated with Hereditary Breast and Ovarian Cancer, however it should be considered that familial co-segregation data has, to our knowledge, yet to be reported. BLAT searches for the intronic sequence surrounding the variant (30 nucleotide sequence surrounding the location of the variant) gave only 1 hit with 100% sequence identity on chromosome 22 (i.e. at the expected location). Therefore, the variant is unlikely to be derived from a CHEK2 pseudogene. Fourteen submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. Eight classified the variant as likely pathogenic (n=7)/pathogenic (n=1), and six classified it as VUS. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Breast carcinoma Uncertain:1

Uncertain significance, flagged submission

clinical testing

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Aug 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	9.2
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Benign	0.63
SpliceAI score (max)		0.90		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.90		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs587782849; hg19: chr22-29120962;