22-28694072-C-T

Variant names:

• chr22-28694072-C-T
• rs121908706
• NM_007194.4:c.1421G>A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PP3_Moderate PP5

The NM_007194.4(CHEK2):​c.1421G>A​(p.Arg474His) variant causes a missense change. The variant allele was found at a frequency of 0.0000457 in 1,596,022 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 0.000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000044 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8 U:11 B:1 O:1
• Conservation: PhyloP100: 5.57

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 3 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.938
• PP5: Variant 22-28694072-C-T is Pathogenic according to our data. Variant chr22-28694072-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 126910.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_benign=1, Likely_pathogenic=8, Uncertain_significance=9, not_provided=1}. Variant chr22-28694072-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.1421G>A	p.Arg474His	missense_variant	Exon 13 of 15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.1421G>A	p.Arg474His	missense_variant	Exon 13 of 15	1	NM_007194.4	ENSP00000385747.1

Frequencies

GnomAD3 genomes AF: 0.0000657 AC: 10 AN: 152154 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

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: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000642 AC: 15 AN: 233796 Hom.: 0 AF XY: 0.0000390 AC XY: 5 AN XY: 128358

Gnomad AFR exome AF: 0.000204

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000330

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000919

Gnomad OTH exome AF: 0.000168

GnomAD4 exome AF: 0.0000436 AC: 63 AN: 1443868 Hom.: 0 Cov.: 30 AF XY: 0.0000487 AC XY: 35 AN XY: 718702

Gnomad4 AFR exome AF: 0.0000300

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000540

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000657 AC: 10 AN: 152154 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74328

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.0000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000642

ESP6500AA AF: 0.000361 AC: 1

ESP6500EA AF: 0.000213 AC: 1

ExAC AF: 0.0000693 AC: 8

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:8 Uncertain:11 Benign:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial cancer of breast Pathogenic:1 Uncertain:4 Benign:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 474 of the CHEK2 protein (p.Arg474His). This variant is present in population databases (rs121908706, gnomAD 0.02%). This missense change has been observed in individual(s) with breast and/or ovarian cancer and non-Hodgkin lymphoma (PMID: 25186627, 25452441, 26506619, 30303537, 30333958, 30613976, 31050813, 34903604, 35534704). This variant is also known as p.Arg517His. ClinVar contains an entry for this variant (Variation ID: 126910). 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 affects CHEK2 function (PMID: 31050813, 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. -

Mar 09, 2023

Myriad Genetics, Inc.

Significance: Likely benign

Review Status: flagged submission

Collection Method: clinical testing

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. -

Feb 07, 2024

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 25, 2017

Counsyl

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R474H variant (also known as c.1421G>A), located in coding exon 12 of the CHEK2 gene, results from a G to A substitution at nucleotide position 1421. The arginine at codon 474 is replaced by histidine, an amino acid with highly similar properties. This alteration has been detected in a familial breast and ovarian cancer patient (reported as c.1550G>A, p.Arg517His under reference sequence NM_001005735.1) and reported in the germline of 1/340 non-Hodgkin lymphoma patients and in 0/445 non-cancer controls (Havranek O et al. PLoS ONE. 2015 Oct;10:e0140819; Brovkina OI et al. Front Oncol. 2018 Oct 2;8:421). This amino acid position is highly conserved in available vertebrate species. This variant has an entry in ClinVar with 9 submissions, one pathogenic, on “not provided”, and 7 uncertain significance, one star. Alternative variant chr22:29090060 C⇒A (Arg474Leu) is classified Likely Pathogenic, 0 stars, by ClinVar In addition, this alteration is predicted to be pathogenic computational verdict based on 12 pathogenic predictions from BayesDel_addAF, DANN, DEOGEN2, EIGEN, FATHMM-MKL, LIST-S2, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFT vs 1 benign prediction from PrimateAI. Therefore, this variant is classified as of uncertain significance. -

May 22, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS3,PM5,PS4_SUP -

not provided Pathogenic:3 Uncertain:1 Other:1

Feb 07, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.1421G>A (p.Arg474His) variant has been reported in the published literature in individuals affected with breast and/or ovarian cancer (PMIDs: 31050813 (2019), 29522266 (2018), 25186627 (2015)), and in one individual with Non-Hodgkins lymphoma (PMID: 26506619 (2015)). Functional evidence suggests that this variant may impact CHEK2 protein function (PMIDs: 34903604 (2021), 31050813 (2019)). The frequency of this variant in the general population, 0.00021 (5/23450 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 predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

Apr 02, 2025

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: decreased autophosphorylation, kinase activity, and protein stability (PMID: 31050813, 34903604, 37449874); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.1550G>A p.(R517H); This variant is associated with the following publications: (PMID: 26506619, 25452441, 31050813, 30303537, 30333958, 30374176, 31422574, 25186627, 30613976, 33471991, 29522266, 25085752, 34903604, 35534704, 34326862, 36288950, 37449874, 38476463, 22419737, 19782031, 39594831, 38496821, 39684258, 38773787) -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CHEK2: PS4, PS3:Moderate, PM2:Supporting -

-

Institute. of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Hereditary cancer-predisposing syndrome Pathogenic:2 Uncertain:2

Oct 02, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces arginine with histidine at codon 474 of the CHEK2 protein. This variant impacts a highly conserved arginine in the kinase domain of the protein (PMID: 15060014, 19782031). Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported that this variant impacts CHEK2 function in kinase assays and DNA damage response performed in mouse embryonic stem cells, yeast and in vitro models (PMID: 30851065, 31050813, 34903604). This variant has been detected in a breast cancer case-control meta-analysis in 18/60466 cases and 0/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID CHEK2_000183). This variant also has been reported in individuals affected with breast cancer (PMID: 25186627, 25452441, 29522266, 30303537), a suspected hereditary breast and ovarian cancer family (PMID: 30333958), an individual affected with non-Hodgkin lymphoma (PMID: 26506619) and an individual without cancer diagnosis (PMID: 31422574). This variant has been identified in 19/265178 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Feb 04, 2025

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3; PS4_SUP -

Jun 15, 2023

Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 29, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R474H variant (also known as c.1421G>A), located in coding exon 12 of the CHEK2 gene, results from a G to A substitution at nucleotide position 1421. The arginine at codon 474 is replaced by histidine, an amino acid with highly similar properties. This alteration has been detected in multiple cohorts of individuals diagnosed with lymphoma, breast, colon and/or ovarian cancer (Havranek O et al. PLoS ONE. 2015 Oct;10:e0140819; Tung N et al. Cancer, 2015 Jan;121:25-33; Brovkina OI et al. Front Oncol. 2018 Oct 2;8:421; Hauke J et al. Cancer Med, 2018 04;7:1349-1358; Girard E et al. Int J Cancer, 2019 04;144:1962-1974; Dorling et al. N Engl J Med. 2021 02;384:428-439; Güleç Ceylan G et al. Tohoku J Exp Med, 2022 Nov;258:319-325). This variant was non-functional in an in vitro kinase assay and a human cell-based kinase assays measuring KAP1 phosphorylation and CHK2 autophosphorylation (Kleiblová P et al. Klin Onkol, 2019;32:36-50; Stolarova L et al. Clin Cancer Res. 2023 Aug;29(16):3037-3050). In a mouse embryonic stem cell-based system, this alteration was found to be damaging to Kap1 phosphorylation (Boonen RACM et al. Cancer Res, 2022 02;82:615-631). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Li-Fraumeni syndrome 2 Pathogenic:1 Uncertain:1

Oct 30, 2023

Zotz-Klimas Genetics Lab, MVZ Zotz Klimas

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 03, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS3,PM5,PS4_SUP -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Nov 11, 2024

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

According to the ACMG SVI adaptation criteria we chose these criteria: PS3 (strong pathogenic): Kleiblova (2019) PMID: 31050813 --> damaging Stolarova (2023) PMID: 37449874 --> damaging, PS4 (supporting pathogenic): Dorling et al. (2020) (PMID: 35585550): in 18/60466 Cases, in 0/53461 Controls, PP3 (medium pathogenic): REVEL (0.867) Pathogenic Moderate -

not specified Uncertain:1

Jul 16, 2024

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.1421G>A (p.Arg474His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.4e-05 in 233796 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome (6.4e-05 vs 0.00031), allowing no conclusion about variant significance. c.1421G>A has been reported in the literature in individuals affected with breast cancer, ovarian cancer, or an unspecified hereditary cancer (e.g. Girard_2019, de Oliveira_2022, Kleiblova_2019, Couch_2015, Rizzolo_2019, Brovkina_2018, Bhai_2021, Akcay_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <20% of normal kinase activity (Kleiblova_2019, Boonen_2022). The following publications have been ascertained in the context of this evaluation (PMID: 32658311, 34326862, 34903604, 30333958, 25452441, 30303537, 26506619, 31050813, 30613976, 30374176, 25186627, 35534704). ClinVar contains an entry for this variant (Variation ID: 126910). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

CHEK2-related disorder Uncertain:1

May 23, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CHEK2 c.1421G>A variant is predicted to result in the amino acid substitution p.Arg474His. This variant has been reported in an individual with non-Hodgkin lymphoma (Havranek et al. 2015. PubMed ID: 26506619), individuals with breast cancer (Couch et al. 2015. PubMed ID: 25452441, Table S6; Tung et al. 2015. PubMed ID: 25186627, Supp. Info; Girard et al. 2019. PubMed ID: 30303537, Table S3), and an individual with ovarian cancer (Kleiblova et al. 2019. PubMed ID: 31050813, Tables 1 and S3, Patient 1380). It has also been reported in an individual with a family history of hereditary breast and/or ovarian cancer (HBOC), but was also found in control individuals (Brovkina et al. 2018. PubMed ID: 30333958, Table 3, referred to as c.1550G>A, p.Arg517His). A variant interpretation study interpreted this variant as uncertain significance (Tsai et al. 2019. PubMed ID: 30374176, Table S1). Functional studies suggest this variant may impair CHK2 kinase catalytic activity (Kleiblova et al. 2019. PubMed ID: 31050813, Figure 2, Table S2). This variant has been reported at a frequency of ~0.02% in individuals of African origin in the gnomAD database. There are conflicting interpretations of pathogenicity ranging from likely pathogenic to likely benign in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/126910/). Based on these observations, the c.1421G>A variant is classified as uncertain. -

Breast and/or ovarian cancer Uncertain:1

Jun 12, 2023

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.39
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.50	D;.;D;.;D;.;D;.;.
Eigen	Pathogenic	0.69
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.97	.;D;.;D;.;D;D;D;.
M_CAP	Uncertain	0.25	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.86	D
MutationAssessor	Pathogenic	4.8	H;.;H;.;H;.;H;.;.
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-4.6	D;D;D;.;D;D;.;D;D
REVEL	Pathogenic	0.87
Sift	Pathogenic	0.0	D;D;D;.;D;D;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;.;D;D;.;D;D
Polyphen		1.0	D;D;D;.;D;D;D;D;D
Vest4		0.96
MVP		0.94
MPC		0.17
ClinPred		0.99	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.95
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs121908706; hg19: chr22-29090060; COSMIC: COSV60420515; COSMIC: COSV60420515;