rs139366548

Positions:

• chr22-28695232-A-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM1 BP4_Strong BP6

The NM_007194.4(CHEK2):​c.1270T>C​(p.Tyr424His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,593,488 control chromosomes in the GnomAD database, including 1 homozygotes. 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. Y424C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00019 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00015 (1 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:21 B:3 O:1
• Conservation: PhyloP100: 7.38

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 -3 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 17 uncertain in NM_007194.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.03749332).
• BP6: Variant 22-28695232-A-G is Benign according to our data. Variant chr22-28695232-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 128054.We mark this variant Likely_benign, oryginal submissions are: {not_provided=1, Likely_benign=3, Uncertain_significance=15}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.1270T>C	p.Tyr424His	missense_variant	12/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.1270T>C	p.Tyr424His	missense_variant	12/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.000191 AC: 29 AN: 152206 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00749

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: 0.000287 AC: 72 AN: 250548 Hom.: 0 AF XY: 0.000273 AC XY: 37 AN XY: 135450

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00607

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000619

Gnomad OTH exome AF: 0.000656

GnomAD4 exome AF: 0.000150 AC: 216 AN: 1441282 Hom.: 1 Cov.: 26 AF XY: 0.000159 AC XY: 114 AN XY: 718344

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00635

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000210

Gnomad4 OTH exome AF: 0.000469

GnomAD4 genome AF: 0.000191 AC: 29 AN: 152206 Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16 AN XY: 74360

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00749

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: 0.000923 Hom.: 0

Bravo AF: 0.000193

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.000280 AC: 34

EpiCase AF: 0.000109

EpiControl AF: 0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:21 Benign:3 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:6 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 25, 2024	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: 19782031, 25186627, 29522266, 28779002, 32546565, 18571837, 22419737, 18085035, 25452441, 25117502, 30154229, 29596542, 30851065, 31050813, 31398194, 31256874, 31784482, 30374176, 33128190, 32866190, 26580448, 36315097, 33471991, 36360192, 36845387, 37449874, 35534704, 37842866, 34326862, 32885271) -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 22, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Familial cancer of breast Uncertain:4 Benign:1

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]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 424 of the CHEK2 protein (p.Tyr424His). This variant is present in population databases (rs139366548, gnomAD 0.6%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with breast, uterine, and prostate cancer (PMID: 18085035, 18571837, 22419737, 30374176). ClinVar contains an entry for this variant (Variation ID: 128054). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 18571837, 22419737, 30851065). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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	Counsyl	Jul 18, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 27, 2024	- -

Hereditary cancer-predisposing syndrome Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 08, 2023	This missense variant replaces tyrosine with histidine at codon 424 of the CHEK2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown the mutant protein to be defective in an ex vivo human cell kinase assay and in one of two in vitro kinase assays (PMID: 31050813) and in two of three yeast complementation assays (PMID: 18571837, 22419737, 30851065). This variant has been reported in individuals affected with breast cancer, colon cancer, and prostate cancer, but also found in control individuals (PMID: 18085035, 18571837, 22419737, 25186627, 25452441, 29596542, 31050813, 33471991, 36315097). This variant has been identified in 74/281950 chromosomes (63/10344 Ashkenazi Jewish 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	curation	Sema4, Sema4	Feb 03, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 19, 2024	The p.Y424H variant (also known as c.1270T>C), located in coding exon 11 of the CHEK2 gene, results from a T to C substitution at nucleotide position 1270. The tyrosine at codon 424 is replaced by histidine, an amino acid with similar properties. This variant, which is present at a high frequency in the Ashkenazi Jewish sub-population, has been identified in several breast and prostate cancer families; however, it does not segregate completely with disease (Laitman Y et al. Isr. Med. Assoc. J. 2007 Nov;9:791-6; Tischkowitz MD et al. Cancer Lett. 2008 Oct;270:173-80; Roeb W et al. Hum. Mol. Genet. 2012 Jun;21:2738-44; Couch FJ et al. J. Clin. Oncol. 2015 Feb;33:304-11; Tung N et al. Cancer 2015 Jan;121(1):25-33; Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879; Dorling et al. N Engl J Med. 2021 02;384:428-439; Kirchner K et al. Genes (Basel), 2022 Oct;13). Yeast-based functional studies conflict about whether or not this variant is deleterious (Tischkowitz MD et al. Cancer Lett. 2008 Oct;270:173-80; Roeb W et al. Hum. Mol. Genet. 2012 Jun;21:2738-44; Delimitsou A et al. Hum Mutat. 2019 05;40:631-648). A functional assay employing a complementation assay in human nontransformed RPE1-CHEK2-knockout cells quantifying CHK2-specific phosphorylation of endogenous protein KAP1A demonstrated <25% CHK2 kinase activity (Kleiblova P et al. Int. J. Cancer 2019 10;145(7):1782-1797). A case-control study suggests that this variant is not associated with prostate cancer; however, the results were not statistically significant (Tischkowitz MD et al. Cancer Lett. 2008 Oct;270:173-80). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Feb 14, 2023	- -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 10, 2023	Variant summary: CHEK2 c.1270T>C (p.Tyr424His) results in a 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 0.00029 in 250548 control chromosomes (gnomAD). The observed variant frequency is approximately 10-fold of the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Li-Fraumeni Syndrome phenotype (2.8e-05), strongly suggesting that the variant is benign. However, this observation needs to be cautiously considered since the majority of occurrences was detected in the Ashkenazi Jewish subpopulation (a confined population, example: DiazVelasquez_2023) and additionally, the variant is located in a region of the gene indicated to be affected by pseudogene interference. c.1270T>C has been reported in the literature in individuals affected with cancer, including breast, prostate, colon and gastric cancer (e.g. Couch_2015, Kleiblova_2019, Laitman_2007, Roeb_2012, Tischkowitz_2008, Tung_2015, Bhai_ATM_Fgene_2021). Family studies carried out by some of these studies demonstrated the variant did not segregate with disease (e.g. Roeb_2012, Tischkowitz_2008). This variant was also present in both case cohort and control cohort in a large study evaluating risk of breast cancer by the Breast Cancer Association Consortium (Dorling_2021). Although, functional studies provided conflicting evidence as to whether the variant has a deleterious or benign effect (Delimitsou_2019, Kleiblova_2019, Roeb_2012, Tischkowitz_2008). The following publications have been ascertained in the context of this evaluation (PMID: 34326862, 31415627, 25452441, 30851065, 36845387, 29596542, 31050813, 18085035, 22419737, 25117502, 18571837, 30374176, 25186627, 26580448, 33471991). 15 have cited clinical-significance assessments for this variant to ClinVar after 2014 as uncertain significance (n=13) and as likely benign (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 02, 2018	- -

CHEK2-related cancer predisposition Uncertain:1 Other: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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not provided, no classification provided	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	Variant reported in multiple Invitae PIN participants by multiple clinical testing laboratories. Variant interpreted as a Variant of Uncertain Significance by all laboratories and reported most recently on 11/29/2018 by Invitae and 12/22/2014 by GeneDx. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -

CHEK2-related disorder Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 16, 2024

The CHEK2 c.1270T>C variant is predicted to result in the amino acid substitution p.Tyr424His. This variant has been reported in individuals with breast cancer, individuals with prostate cancer, and individuals undergoing clinical diagnostic testing (Table 1,Laitman et al. 2007. PubMed ID: 18085035; Table S1, Selkirk et al. 2014. PubMed ID: 25117502; Table S1, Tung et al. 2014. PubMed ID: 25186627; Table S6, Couch et al. 2014. PubMed ID: 25452441; Table S1, Lerner-Ellis et al. 2020. PubMed ID: 32885271; Table 2, Gomes et al. 2020. PubMed ID: 33128190; Figure 1, Kirchner et al. 2022. PubMed ID: 36360192). It has been reported in individuals of Ashkenazi Jewish descent with unspecified cancer histories (Table 2, Diaz-Velasquez et al. 2023. PubMed ID:36845387). It has been observed as a germline variant in a colorectal cancer tumor (eWorksheet, ID# 403, Hampel et al. 2018. PubMed ID: 29596542). The results of in vitro and in vivo (yeast) experimental studies of this variant are conflicting (Figure 1, Tischkowitz et al. 2008. PubMed ID: 18571837; Table 1, Roeb et al. 2012. PubMed ID: 22419737; Delimitsou et al. 2019. PubMed ID: 30851065; Table 1, Kleiblova et al. 2019. PubMed ID: 31050813). This variant is reported in 0.61% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. It is interpreted as uncertain significance by the vast majority of submitters in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/128054/). 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

Feb 27, 2023

- -

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

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 23, 2017

- -

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.Tyr424His variant was identified in 6 of 496 proband chromosomes (frequency: 0.0121) from individuals or families with hereditary breast and ovarian cancer (Laitman 2007, Tischkowitz 2008). The variant was also identified in the following databases: dbSNP (ID: rs139366548) as “With Uncertain significance allele”, ClinVar (as uncertain significance by GeneDx, Ambry Genetics, Invitae, Color Genomics, and Quest Diagnostics), and Clinvitae (3x). The variant was not identified in Cosmic, MutDB, or the Zhejiang Colon Cancer Database. The variant was identified in control databases in 70 of 276482 chromosomes at a frequency of 0.000253 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: Other in 3 of 6444 chromosomes (freq: 0.000466), European (Non-Finnish) in 7 of 126180 chromosomes (freq: 0.000055), and Ashkenazi Jewish in 60 of 10128 chromosomes (freq: 0.005924); it was not observed in the African, Latino, East Asian, European (Finnish), and South Asian populations. There are conflicting classifications of this variant in the literature. Roeb (2012) conducted a yeast-based in vivo functional assay and found the variant damaging. They also found that co-segregation of the variant with breast cancer in families is consistent with expectation for damaging alleles of moderate penetrance (Roeb 2012). Another study by Tischkowitz (2008) found the variant occurred in nine affected cases from four different families; however it did not completely segregate with the disease. Functional assays using S. Cerevisae revealed that the p.Tyr424His substitution did not alter function of CHEK2 protein; although the p.Tyr424His variant occurs at a highly conserved position, it does not seem to play a significant role in predisposition to prostate cancer (Tischkowitz 2008). They concluded that while the results do not exclude the possibility that this is a modest-risk predisposition allele in the Ashkenazi Jewish population, functional studies in yeast indicate that the variant does not have a significant deleterious effect (Tischkowitz 2008). The p.Tyr424His residue is conserved in mammals, but not in lower organisms, and the variant amino acid Histidine (His) is present in S. cerevisiae (Brewer’s yeast), increasing the likelihood that this variant does not have clinical significance. 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. 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. -

Hereditary breast ovarian cancer syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

curation

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

Apr 09, 2024

widersprüchliche funkt. Daten siehe Mail Lisa W. (Daten einfügen); According to the ACMG SVI adaptation criteria we chose this criterion: PS3 (supporting pathogenic): widersprüchliche funkt. Daten -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Pathogenic	0.22
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.24	T;.;T;.;T;.;T;.;.
Eigen	Uncertain	0.62
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.97	.;D;.;D;.;D;D;D;.
M_CAP	Benign	0.084	D
MetaRNN	Benign	0.037	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.46	T
MutationAssessor	Benign	0.54	N;.;N;.;N;.;N;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-3.6	D;D;D;.;D;D;.;D;D
REVEL	Uncertain	0.62
Sift	Uncertain	0.016	D;D;D;.;D;D;.;T;D
Sift4G	Benign	0.067	T;D;T;.;T;T;.;D;D
Polyphen		0.93	P;D;P;.;P;D;P;D;D
Vest4		0.76
MVP		0.58
MPC		0.17
ClinPred		0.18	T
GERP RS		5.8
Varity_R		0.85
gMVP		0.76

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: rs139366548; hg19: chr22-29091220;