22-28725013-T-G

Variant names:

• chr22-28725013-T-G
• rs146198085
• NM_007194.4:c.556A>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3 BP6

The NM_007194.4(CHEK2):​c.556A>C​(p.Asn186His) variant causes a missense change. The variant allele was found at a frequency of 0.000144 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000092 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:23 B:2
• Conservation: PhyloP100: 5.73

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 Uncertain_significance. Variant got 0 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.756
• BP6: Variant 22-28725013-T-G is Benign according to our data. Variant chr22-28725013-T-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 141977.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=14}. Variant chr22-28725013-T-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.556A>C	p.Asn186His	missense_variant	Exon 4 of 15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.556A>C	p.Asn186His	missense_variant	Exon 4 of 15	1	NM_007194.4	ENSP00000385747.1

Frequencies

GnomAD3 genomes AF: 0.0000920 AC: 14 AN: 152100 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

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: 0.000176

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000597 AC: 15 AN: 251420 Hom.: 0 AF XY: 0.0000515 AC XY: 7 AN XY: 135898

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000114

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000150 AC: 219 AN: 1461846 Hom.: 0 Cov.: 32 AF XY: 0.000140 AC XY: 102 AN XY: 727220

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000192

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome AF: 0.0000920 AC: 14 AN: 152100 Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7 AN XY: 74300

Gnomad4 AFR AF: 0.0000483

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: 0.000176

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000226 Hom.: 0

Bravo AF: 0.0000567

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000659 AC: 8

EpiCase AF: 0.000164

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:23 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:10 Benign:1

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Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Jul 09, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.556A>C; p.Asn186His variant (rs146198085, ClinVar Variation ID: 141977), also known as p.Asn229His for NM_001005735, is reported in the literature in individuals affected with breast cancer (Aloraifi 2015, Decker 2017, Girard 2019, Hilbers 2020, Tung 2015). Additionally, this variant was found in an individual with a personal and family history of breast cancer that carried an ATM variant (Bhai 2021). This variant is found in the general population with an overall allele frequency of 0.007% (19/282,804 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is deleterious (REVEL: 0.713). Functional analyses in a yeast-based assay following DNA damage showed similar growth compared to wildtype (Delimitsou 2019). Additionally, in a mouse embryonic stem cell assay, this variant demonstrated similar expression and activity compared to wildtype (Boonen 2022). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Aloraifi F et al. Detection of novel germline mutations for breast cancer in non-BRCA1/2 families. FEBS J. 2015 Sep;282(17):3424-37. PMID: 26094658. Bhai P et al. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet. 2021 Jul 13;12:698595. PMID: 34326862. Boonen RACM et al. Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. Cancer Res. 2022 Feb 15;82(4):615-631. PMID: 34903604. Decker B et al. Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. J Med Genet. 2017 Nov;54(11):732-741. PMID: 28779002. Delimitsou A et al. Functional characterization of CHEK2 variants in a Saccharomyces cerevisiae system. Hum Mutat. 2019 May;40(5):631-648. PMID: 30851065. Girard E et al. Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. Int J Cancer. 2019 Apr 15;144(8):1962-1974. PMID: 30303537. Hilbers FS et al. Clustering of known low and moderate risk alleles rather than a novel recessive high-risk gene in non-BRCA1/2 sib trios affected with breast cancer. Int J Cancer. 2020 Nov 15;147(10):2708-2716. PMID: 32383162. Tung N et al. Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Cancer. 2015 Jan 1;121(1):25-33. PMID: 25186627. -

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Jul 24, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.556A>C (p.Asn186His) variant has been reported in the published literature in individuals with breast cancer (PMIDs: 34326862 (2021), 32383162 (2020), 30303537 (2019), 26094658 (2015), 25186627 (2015)). In multiple large-scale breast cancer association studies, this variant was observed in individuals with breast cancer and reportedly healthy individuals (PMIDs: 33471991 (2021) see also LOVD (https://databases.lovd.nl/shared/variants/CHEK2), 28779002 (2017)). Experimental evidence suggests this variant does not impact protein function (PMIDs: 34903604 (2021), 30851065 (2019)), however not all critical CHEK2 protein functions were not assessed. The frequency of this variant in the general population, 0.00012 (16/129134 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CHEK2: BS3:Supporting -

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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 28, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Identified in individuals with breast and other cancers as well as in controls, and segregation was incomplete in one breast cancer family (Tung et al., 2015; Decker et al., 2017; Girard et al., 2019; Hilbers et al., 2020; Song et al., 2021); Published functional studies suggest no damaging effect: no impact on kinase activity in a mouse ES cell-based system and growth rates similar to wild type following DNA damage in a yeast-based assay (Delimitsou et al., 2019; Boonen et al., 2022); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26094658, 30303537, 28873162, 28825729, 28779002, 32383162, 30374176, 32546565, 30851065, 25186627, 34903604, 19782031, 22419737) -

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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Familial cancer of breast Uncertain:4

Sep 01, 2016

Counsyl

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 09, 2023

Myriad Genetics, Inc.

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk. -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces asparagine, which is neutral and polar, with histidine, which is basic and polar, at codon 186 of the CHEK2 protein (p.Asn186His). This variant is present in population databases (rs146198085, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer and/or pleomorphic xanthoastrocytoma and meningioma (PMID: 26094658, 30303537, 30374176, 32383162, 34903604). This variant is also known as c.685T>G (p.Asn229His). ClinVar contains an entry for this variant (Variation ID: 141977). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change does not substantially affect CHEK2 function (PMID: 30851065, 34903604). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Jul 27, 2022

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

_x000D_ Criteria applied: PM2_SUP, PP3 -

not specified Uncertain:2

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Feb 24, 2025

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CHEK2 c.556A>C (p.Asn186His) results in a conservative amino acid change located in the Forkhead-associated (FHA) domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6e-05 in 251420 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome (6e-05 vs 0.00031), allowing no conclusion about variant significance. c.556A>C has been reported in the literature in individuals affected with breast cancer (e.g. Aloraifi_2015, Tung_2015, Girard_2019, van der Merwe_2022). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least two publications report experimental evidence evaluating an impact on protein function. One study showed no damaging effect of this variant in a yeast-based assay (Delimitsou_2019), while another showed reduced phosphorylation of KAP1 (Stolarova_2023). The following publications have been ascertained in the context of this evaluation (PMID: 26094658, 30851065, 38378842, 30303537, 37449874, 25186627, 36568162). ClinVar contains an entry for this variant (Variation ID: 141977). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Hereditary breast ovarian cancer syndrome Uncertain:2

Feb 18, 2025

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

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Apr 19, 2022

National Health Laboratory Service, Universitas Academic Hospital and University of the Free State

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Uncertain:1 Benign:1

Jun 04, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces asparagine with histidine at codon 186 of the CHEK2 protein. this variant is also known as p.Asn229His in the literature based on an alternate transcript NM_001005735. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown the mutant protein to exhibit normal CHEK2 protein expression and function in yeast and mouse embryonic stem cells (PMID: 30851065, 34903604), although one study in CHEK2-deficient human cells showed impaired KAP1 phosphorylation and intermediate CHEK2 autophosphorylation (PMID: 37449874). This variant has been reported in two individuals affected with breast cancer (PMID: 25186627, 26094658). In two large breast cancer case-control meta-analyses, this variant has been observed in 27/60439 individuals affected with breast cancer and 15/53446 controls (OR=1.592, 95%CI 0.847 to 2.993; PMID: 33471991) and 8/73048 individuals affected with breast cancer and 20/88658 controls (OR =0.4855, 95%CI 0.2138 to 1.1023; PMID: 37449874). This variant has been identified in 19/282804 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Jul 30, 2020

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

CHEK2-related disorder Uncertain:1

May 03, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CHEK2 c.556A>C variant is predicted to result in the amino acid substitution p.Asn186His. This variant has been reported in individuals with breast cancer and an individual undergoing genetic testing (Supplement, Tung et al. 2015. PubMed ID: 25186627; Table S1, referred to as c.685T>G, p.Asn229His, Aloraifi et al. 2015. PubMed ID: 26094658; Table S3, Girard et al. 2018. PubMed ID: 30303537; Table S1, Tsai et al. 2018. PubMed ID: 30374176). In vivo experimental investigation using a yeast based assay suggest this variant is benign (Table 1, Delimitsou et al. 2019. PubMed ID: 30851065). This variant is reported in 0.012% of alleles in individuals of European (Non-Finnish) descent in gnomAD. It is interpreted as uncertain significance by the vast majority of submitters to ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/141977/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Familial cancer of breast;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C5882668:Li-Fraumeni syndrome 2 Uncertain:1

May 23, 2017

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Predisposition to cancer Uncertain:1

Nov 27, 2024

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.556A>C (p.Asn186His) missense change has a maximum subpopulation frequency of 0.01% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL predicts a deleterious effect on protein function, however a functional study suggests this variant does not impact protein function (PMID: 30851065). To our knowledge, this variant has not been reported as pathogenic in individuals with CHEK2-related tumors. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance. -

Endometrial carcinoma Uncertain:1

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Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CHEK2 p.Asn186His variant was identified in 1 of 208 proband chromosomes (frequency: 0.005) from individuals or families with non-BRCA1/2 breast cancer and was not identified in 202 control chromosomes from healthy individuals (Aloraifi 2015). The variant was identified in dbSNP (ID: rs146198085) as “With Uncertain significance allele”, in ClinVar (classified with conflicting interpretations of pathogenicity: likely benign by Laboratory Corporation of America; and uncertain significance by Ambry Genetics, GeneDx, Invitae, Counsyl, Fulgent Genetics and Color Genomics Inc), Clinvitae (4x), Cosmic (1x in a wilms tumour), and Zhejiang Colon Cancer Database (1x), but was not found in MutDB. The variant was also identified in control databases in 18 of 277188 chromosomes at a frequency of 0.00007 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 3 of 24028 chromosomes (freq: 0.0001), and European Non-Finnish in 15 of 126684 chromosomes (freq: 0.0001); it was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Asn186 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact of the variant His to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.017	T
BayesDel_noAF	Uncertain	-0.030
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.60	D;.;D;D;.;D;.;.;D
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	.;D;.;.;D;D;.;D;D
M_CAP	Benign	0.057	D
MetaRNN	Pathogenic	0.76	D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.71	D
MutationAssessor	Uncertain	2.8	M;M;M;M;.;M;M;.;.
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-4.4	D;D;D;D;D;.;D;D;.
REVEL	Pathogenic	0.71
Sift	Uncertain	0.0030	D;D;D;D;D;.;D;D;.
Sift4G	Uncertain	0.0090	D;D;D;D;D;.;D;D;D
Polyphen		1.0	D;D;D;D;D;D;D;.;.
Vest4		0.73
MVP		0.95
MPC		0.16
ClinPred		0.52	D
GERP RS		5.9
Varity_R		0.93
gMVP		0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs146198085; hg19: chr22-29121001; COSMIC: COSV60416123; COSMIC: COSV60416123;