rs199749372

Variant names:

• chr22-28719417-T-C
• rs199749372
• NM_007194.4:c.661A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-28719417-T-C
• chr22-28719417-T-G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 0P and 3B. BP4_Moderate BS2_Supporting

The NM_007194.4(CHEK2):​c.661A>G​(p.Ile221Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,591,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict 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. I221M) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8 B:1
• Conservation: PhyloP100: 2.97
• Publications: 9 publications found

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]

CHEK2 Gene-Disease associations (from GenCC):

• CHEK2-related cancer predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• Li-Fraumeni syndrome 2

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• acute myeloid leukemia

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• familial ovarian cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.11908299).
• BS2: High AC in GnomAdExome4 at 15 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.661A>G	p.Ile221Val	missense_variant	Exon 5 of 15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.661A>G	p.Ile221Val	missense_variant	Exon 5 of 15	1	NM_007194.4	ENSP00000385747.1

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152172 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

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: 0.0000441

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000131 AC: 3 AN: 229264 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000315

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000196

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000104 AC: 15 AN: 1439110 Hom.: 0 Cov.: 27 AF XY: 0.0000126 AC XY: 9 AN XY: 715084

African (AFR) AF: 0.00 AC: 0 AN: 33058

American (AMR) AF: 0.0000236 AC: 1 AN: 42308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25352

East Asian (EAS) AF: 0.0000254 AC: 1 AN: 39396

South Asian (SAS) AF: 0.00 AC: 0 AN: 83162

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52260

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5162

European-Non Finnish (NFE) AF: 0.0000118 AC: 13 AN: 1098994

Other (OTH) AF: 0.00 AC: 0 AN: 59418

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152290 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74484

African (AFR) AF: 0.00 AC: 0 AN: 41556

American (AMR) AF: 0.00 AC: 0 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68020

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.0000329 Hom.: 0

Bravo AF: 0.0000151

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000117 AC: 1

ExAC AF: 0.0000249 AC: 3

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:8 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:3 Benign:1

Jul 18, 2022

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional study demonstrates no damaging effect: normal cell growth after MMS-induced DNA damage (Delimitsou et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as c.790A>G, p.Ile264Val; This variant is associated with the following publications: (PMID: 27978560, 31398194, 31241222, 31106920, 30851065, 19782031, 22419737, 29769011) -

Apr 10, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.661A>G (p.Ile221Val) variant has been reported in the published literature in individuals with breast cancer (PMIDs: 33471991 (2021), 31206626 (2019), 28779002 (2017)), colorectal cancer (PMIDs: 28944238 (2017), 27978560 (2016)), and in reportedly healthy individuals (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared)). Experimental studies indicate this variant has neutral to partial effect on CHEK2 protein function (PMIDs: 37449874 (2023), 30851065 (2019)). The frequency of this variant in the general population, 0.000026 (3/117518 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 benign. Based on the available information, we are unable to determine the clinical significance of this variant. -

Feb 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CHEK2: BP1, BP4, BS3:Supporting -

Apr 26, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.661A>G; p.Ile221Val variant (rs199749372), to our knowledge, is not reported in the medical literature but is reported by multiple laboratories in ClinVar (Variation ID: 140835). This variant is found in the general population with an overall allele frequency of 0.003% (1/30956 alleles) in the Genome Aggregation Database. The isoleucine at codon 221 is moderately conserved but computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. However, given the lack of clinical and functional data, the significance of the p.Ile221Val variant is uncertain at this time. -

Familial cancer of breast Uncertain:2

Jan 19, 2024

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 28, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 221 of the CHEK2 protein (p.Ile221Val). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with breast cancer, colorectal cancer, and/or prostate cancer (PMID: 27978560, 28779002, 28944238, 31206626, 32832836). ClinVar contains an entry for this variant (Variation ID: 140835). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 30851065, 37449874). 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. -

Hereditary cancer-predisposing syndrome Uncertain:2

Aug 30, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.I221V variant (also known as c.661A>G), located in coding exon 4 of the CHEK2 gene, results from an A to G substitution at nucleotide position 661. The isoleucine at codon 221 is replaced by valine, an amino acid with highly similar properties. This alteration behaved as functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum Mutat, 2019 05;40:631-648). In another functional study assessing CHEK2-complementation in human RPE1-CHEK2-knockout cells, this alteration was reported as functional through quantification of CHK2 autophosphorylation but intermediate in KAP1 phosphorylation (Stolarova L et al. Clin Cancer Res, 2023 Aug;29:3037-3050). This variant has been reported in cohorts of individuals with early onset colon cancer (Pearlman R et al. JAMA Oncol, 2017 Apr;3:464-471; DeRycke MS et al. Mol Genet Genomic Med, 2017 Sep;5:553-569), African American males with prostate cancer (Matejcic M et al. JCO Precis Oncol, 2020 Jan;4:32-43), and breast cancer cases and controls (Decker B et al. J Med Genet, 2017 11;54:732-741, Weitzel JN et al. Cancer, 2019 Aug;125:2829-2836; Dorling L et al. N Engl J Med, 2021 Feb4;384(5):428-39). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Mar 17, 2025

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces isoleucine with valine at codon 221 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function. Functional studies have shown this variant to have a neutral effect on CHEK2 DNA damage repair activity in a yeast complementation assay (PMID: 30851065), and intermediate impact on KAP1 phosphorylation and neutral impact CHEK2 autophosphorylation in a mammalian cell complementation assay (PMID: 37449874). This variant has been reported in an individual affected with colorectal cancer (PMID: 27978560). In a large breast cancer case-control meta-analysis, this variant was reported in 4/73048 cases and 2/88658 unaffected controls (PMID: 37449874). This variant has been identified in 4/260646 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. -

CHEK2-related disorder Uncertain:1

Jun 01, 2023

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CHEK2 c.661A>G variant is predicted to result in the amino acid substitution p.Ile221Val. This variant has been reported in an individual with colorectal cancer and in a breast cancer cohort study (eTable 2, Pearlman et al. 2017. PubMed ID: 27978560; Table S5, Decker et al. 2017. PubMed ID: 28779002). Experimental studies using a yeast-based assay suggest this variant is benign (Table 1, Delimitsou et al. 2019. PubMed ID: 30851065). This variant is reported in 0.0031% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-29115405-T-C). It is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/140835/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.057	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.091	T;.;T;T;.;T;.;.;.
Eigen	Benign	-0.10
Eigen_PC	Benign	0.088
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.81	.;T;.;.;T;T;T;.;D
M_CAP	Benign	0.0063	T
MetaRNN	Benign	0.12	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.090	N;N;N;N;.;N;.;N;.
PhyloP100		3.0
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	0.11	N;N;N;N;N;.;N;N;N
REVEL	Benign	0.13
Sift	Benign	0.28	T;T;T;T;T;.;T;T;T
Sift4G	Benign	0.50	T;T;T;T;T;.;T;T;T
Polyphen		0.015	B;P;B;B;B;B;P;P;.
Vest4		0.56
MVP		0.45
MPC		0.021
ClinPred		0.19	T
GERP RS		5.5
Varity_R		0.25
gMVP		0.31
Mutation Taster		=61/39	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs199749372; hg19: chr22-29115405;