22-28699893-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_007194.4(CHEK2):c.953G>A(p.Arg318His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R318C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000047 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:13 O:1
• Conservation: PhyloP100: 2.35

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_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.2139971).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.953G>A	p.Arg318His	missense_variant	9/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.953G>A	p.Arg318His	missense_variant	9/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 152084 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

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: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000477 AC: 12 AN: 251482 Hom.: 0 AF XY: 0.0000368 AC XY: 5 AN XY: 135914

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000527

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000465 AC: 68 AN: 1461850 Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30 AN XY: 727220

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000134

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000329 AC: 5 AN: 152084 Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2 AN XY: 74294

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000656

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000105 Hom.: 0

Bravo AF: 0.0000491

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.0000576 AC: 7

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 22, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jan 20, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 318 of the CHEK2 protein (p.Arg318His). This variant is present in population databases (rs143611747, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer (PMID: 22419737, 26845104, 28580595, 34933735, 35264596). This variant is also known as Arg361His. ClinVar contains an entry for this variant (Variation ID: 133890). 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 tolerated. Experimental studies have shown that this missense change affects CHEK2 function (PMID: 22419737). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Division of Medical Genetics, University of Washington	May 06, 2019	The c.953G>A variant has been reported in individuals with familial breast cancer (Roeb 2012, Shirts 2016). The c.953G>A variant has an overall allele frequency of 0.00004 in the Broad Institute ExAC Browser (http://exac.broadinstitute.org/). In silico analyses indicate this is an evolutionarily conserved residue. Thus, it is unknown at this time whether this variant increases cancer risk. -

Hereditary cancer-predisposing syndrome Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 07, 2023	This missense variant replaces arginine with histidine at codon 318 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). A functional study has shown the mutant protein to exhibit an intermediate functional deficit in a DNA damage repair assay in yeast (PMID: 22419737). This variant has been reported in individuals affected with familial breast cancer (PMID 22419737, 26845104, 28580595), but has also been found in healthy cohorts (PMID 24728327, 30303537, https://whi.color.com/variant/22-29095881-C-T). In a large international case-control study, this variant was reported in 13/60466 breast cancer cases and 5/53461 controls (OR=2.299, 95%CI 0.82 to 6.449, p-value=0.155; PMID: 33471991). This variant has been identified in 13/282864 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	May 05, 2023	The p.R318H variant (also known as c.953G>A), located in coding exon 8 of the CHEK2 gene, results from a G to A substitution at nucleotide position 953. The arginine at codon 318 is replaced by histidine, an amino acid with highly similar properties. This variant was detected in an individual diagnosed with early-onset prostate cancer (<59 years of age); authors note that this finding is likely a germline mutation, but could represent an early somatic event (Dong X et al. Am. J. Hum. Genet. 2003 Feb;72(2):270-80). This alteration has been identified in multiple breast cancer cohorts as well as in controls (Shirts BH et al. Genet Med. 2016 10;18:974-81; Girard E et al. Int J Cancer. 2019 04;144:1962-1974; Dorling et al. N Engl J Med. 2021 02;384:428-439; Abdel-Razeq H et al. Front Oncol, 2022 Mar;12:673094; Guindalini RSC et al. Sci Rep, 2022 Mar;12:4190). This alteration was also seen in 0/732 breast cancer patients, 1/189 colorectal cancer patients and 0/490 cancer-free elderly controls in a Turkish population (Akcay IM et al. Int J Cancer, 2021 Jan;148:285-295). In a yeast in vivo study, p.R318H resulted in an intermediate response to DNA damage compared to wild-type (Roeb W et al. Hum. Mol. Genet. 2012 Jun;21(12):2738-44). This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Dec 08, 2021	- -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 29, 2023	Published functional studies are inconclusive: intermediate response to DNA damage (Roeb et al., 2012); 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); This variant is associated with the following publications: (PMID: 26845104, 24728327, 12533788, 29872864, 28580595, 30303537, 35402282, 22419737, 19782031, 34933735, 33471991, 32658311, 35264596) -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2020	- -

not specified Uncertain:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 07, 2020	Variant summary: CHEK2 c.953G>A (p.Arg318His) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.5e-05 in 256088 control chromosomes (gnomAD and publications). This frequency is not significantly higher than expected for a pathogenic variant in CHEK2 causing Hereditary Breast and Ovarian Cancer Syndrome (5.5e-05 vs 0.00031), allowing no conclusion about variant significance. The variant has been reported in the literature in association with familial breast cancer and prostate cancer (Roeb_2012, Dong_2003, Haiman_2013, Shirts_2016, Xie_2018) and an in vitro functional assay demonstrated an intermediate level of DNA damage repair in yeast cells (Roeb_2012). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Six other ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -

CHEK2-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 30, 2024

The CHEK2 c.953G>A variant is predicted to result in the amino acid substitution p.Arg318His. This variant has been reported in multiple individuals with breast cancer (Shirts et al. 2016. PubMed ID: 26845104; Xie et al. 2018. PubMed ID: 28580595; Guindalini et al. 2022. PubMed ID: 35264596; Abdel-Razeq et al. 2022. PubMed ID: 35402282) and at least one individual with colorectal cancer (Akcay et al. 2021. PubMed ID: 32658311); however, this variant has also been observed in multiple healthy control individuals with no reported cancer history (see for example, Girard et al. 2019. PubMed ID: 30303537; Breast Cancer Consortium et al. 2021. PubMed ID: 33471991). A yeast-based DNA-damage repair assay was inconclusive with the p.Arg318His allele retaining 47% residual activity relative to wild type (Table 1, Roeb et al. 2012. PubMed ID: 22419737). This variant is reported in 0.011% of alleles in individuals of Latino descent in gnomAD and is listed in ClinVar as a variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/133890/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Breast and/or ovarian cancer Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

May 30, 2022

- -

Familial cancer of breast;C0346629:Colorectal cancer;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C1836482:Li-Fraumeni syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.081	T
BayesDel_noAF	Benign	-0.13
Cadd	Uncertain	23
Dann	Uncertain	0.99
DEOGEN2	Benign	0.17	T;.;T;.;T;.;T;.;.;.;.;.
Eigen	Benign	0.031
Eigen_PC	Benign	0.19
FATHMM_MKL	Benign	0.57	D
M_CAP	Benign	0.0092	T
MetaRNN	Benign	0.21	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.59	N;N;N;.;N;.;N;.;N;.;.;.
MutationTaster	Benign	0.91	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.3	N;N;N;.;N;N;.;N;N;N;.;D
REVEL	Benign	0.18
Sift	Benign	0.090	T;D;T;.;T;T;.;T;D;T;.;D
Sift4G	Benign	0.29	T;T;T;.;T;T;.;T;T;T;.;.
Polyphen		0.041	B;B;B;.;B;B;B;B;B;.;.;.
Vest4		0.60
MVP		0.62
MPC		0.021
ClinPred		0.078	T
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.26
gMVP		0.41

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: rs143611747; hg19: chr22-29095881; COSMIC: COSV60422390;