rs199708878

Positions:

• chr22-28734715-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_007194.4(CHEK2):​c.7C>T​(p.Arg3Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,612,918 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00014 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8 B:7
• Conservation: PhyloP100: 2.88

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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.01741594).
• BP6: Variant 22-28734715-G-A is Benign according to our data. Variant chr22-28734715-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 142209.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=6, Uncertain_significance=7, Benign=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.7C>T	p.Arg3Trp	missense_variant	2/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.7C>T	p.Arg3Trp	missense_variant	2/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.000139 AC: 21 AN: 151442 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000660

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000442

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.000278 AC: 68 AN: 244816 Hom.: 1 AF XY: 0.000249 AC XY: 33 AN XY: 132754

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000290

Gnomad ASJ exome AF: 0.00455

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.000360

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000740

Gnomad OTH exome AF: 0.000166

GnomAD4 exome AF: 0.000135 AC: 198 AN: 1461358 Hom.: 0 Cov.: 33 AF XY: 0.000154 AC XY: 112 AN XY: 726934

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00451

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000278

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000342

Gnomad4 OTH exome AF: 0.000281

GnomAD4 genome AF: 0.000139 AC: 21 AN: 151560 Hom.: 0 Cov.: 31 AF XY: 0.000176 AC XY: 13 AN XY: 73998

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000659

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000210

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000442

Gnomad4 OTH AF: 0.000475

Alfa AF: 0.000262 Hom.: 0

Bravo AF: 0.000110

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.000231 AC: 28

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:8 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial cancer of breast Uncertain:2 Benign:2

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Jun 15, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 09, 2023	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]. -

Hereditary cancer-predisposing syndrome Uncertain:1 Benign:3

Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	Jan 20, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 09, 2020	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 16, 2021	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Jan 24, 2023	- -

not specified Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 02, 2022	Variant summary: CHEK2 c.7C>T (p.Arg3Trp) results in a non-conservative amino acid change in 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 0.00028 in 251936 control chromosomes, predominantly at a frequency of 0.00036 within the South Asian subpopulation in the gnomAD database, including 1 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 1.15 fold of the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (0.00031), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. c.7C>T has been reported in the literature in individuals affected with Breast and Ovarian Cancer as well as LFS, prostate cancer, and diffuse large B cell lymphoma without strong evidence for causality/neutral outcome (example, Lee_2001, Laitman_2007, Bell_2007, Tischowitz_2008, deMiranda_2013, Tung_2014, Rummel_2017, Kleiblova_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Multiple publications reporting experimental evidence evaluating an impact on protein function indicate that the variant demonstrated kinase activity and growth in yeast comparable to wild-type (Lee_2001, Kleiblova_2019, Delimitsou_2019), while an additional study showed the variant to have a mildly reduced response to DNA damage (Roeb_2012). Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, one of whom reports a likely benign outcome. Based on the evidence outlined above, the variant was classified as likely benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -

not provided Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 08, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2023	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate no damaging effect: most show no or minimal impact on DNA damage response/kinase activity (Lee et al., 2001; Bell et al., 2007; Roeb et al., 2012; Delimitsou et al., 2019; Kleiblova et al., 2019); Observed in individuals with CHEK2-related and other cancers, but also observed in unaffected controls (Lee et al., 2001; Bell et al., 2007; Laitman et al., 2007; Tischkowitz et al., 2008; Rummel et al., 2017); This variant is associated with the following publications: (PMID: 17721994, 22419737, 14569133, 19338683, 23960188, 12610780, 27273131, 31398194, 16080966, 11719428, 18085035, 18571837, 28211887, 28503720, 28873162, 25186627, 24482476, 26296696, 28553140, 30851065, 31050813) -

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

Jun 18, 2020

- -

CHEK2-related cancer predisposition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The CHEK2 p.Arg3Trp variant was identified in 7 of 6118 proband chromosomes (frequency: 0.001) from individuals or families with breast cancer, prostate cancer, Li-Fraumeni Syndrome or diffuse large B-cell lymphomas and was identified in 2 of 7128 control chromosomes from healthy individuals (Bell 2007, Laitman 2007, Lee 2001, Miranda 2013, Rummel 2017, Schutte 2003, Tischkowitz 2008). The variant was also identified in dbSNP (ID: rs199708878 as "With Uncertain significance allele"), ClinVar (classified as uncertain significance by Ambry Genetics, GeneDx, Invitae, Counsyl, Color Genomics, and Integrated Genetics/Laboratory Corporation of America), and the Zhejiang University Database (4x). The variant was not identified in MutDB database. The variant was identified in control databases in 71 of 270350 chromosomes (1 homozygous) at a frequency of 0.0003 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Other in 2 of 6344 chromosomes (freq: 0.0003), Latino in 1 of 34306 chromosomes (freq: 0.00003), European in 7 of 120922 chromosomes (freq: 0.0001), Ashkenazi Jewish in 48 of 9970 chromosomes (freq: 0.01), East Asian in 2 of 18812 chromosomes (freq: 0.0001), and South Asian in 11 of 30678 chromosomes (freq: 0.0004), while the variant was not observed in the African, and Finnish populations. The p.Arg3 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact 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. The variant showed intermediate DNA damage response in CHEK2-mediated DNA damage response assay (Roeb 2012). However, the variant did not show LOH in a primary tumor specimen and demonstrated kinase activity and protein half-life comparable with that of the wild-type protein; the primary tumor assayed was also found to have a homozygous somatic variant in TP53 (Lee 2001). 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	Benign	0.24
BayesDel_addAF	Uncertain	0.064	T
BayesDel_noAF	Pathogenic	0.16
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.18	T;.;T;T;.;T;.;.;.;.;T;.;T
Eigen	Uncertain	0.21
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.91	D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.017	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.46	D
MutationAssessor	Benign	1.1	L;L;L;L;L;L;L;L;.;.;.;.;.
MutationTaster	Benign	1.0	D;N;N;N;N;N;N;N;N;N;N
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-1.2	N;N;N;N;N;.;N;N;N;N;D;.;N
REVEL	Uncertain	0.33
Sift	Uncertain	0.0020	D;D;D;D;D;.;D;D;D;D;D;.;D
Sift4G	Uncertain	0.0040	D;D;D;D;D;.;D;D;D;D;D;.;.
Polyphen		0.97	D;D;D;D;D;D;D;D;.;.;.;.;.
Vest4		0.56
MVP		0.99
MPC		0.083
ClinPred		0.076	T
GERP RS		3.3
Varity_R		0.11
gMVP		0.27

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: rs199708878; hg19: chr22-29130703; COSMIC: COSV60424885; COSMIC: COSV60424885;