chr22-28734447-G-C

Position:

• chr22-28734447-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_007194.4(CHEK2):​c.275C>G​(p.Pro92Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,808 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P92H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:5
• Conservation: PhyloP100: 4.55

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.275C>G	p.Pro92Arg	missense_variant	2/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.275C>G	p.Pro92Arg	missense_variant	2/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461808 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727198

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 07, 2023	This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 92 of the CHEK2 protein (p.Pro92Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 23806170). ClinVar contains an entry for this variant (Variation ID: 410028). 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. 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	Baylor Genetics	Oct 27, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense c.275C>G p.Pro92Arg variant in the CHEK2 gene has been observed in individuals with breast cancer Rashid, Muhammad U et al.,2013. The variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. It is submitted to ClinVar as Uncertain Significance. The amino acid Proline at position 92 is changed to a Arginine changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Pro92Arg in CHEK2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Additional studies in multiple affected individuals and functional evidences are required to prove the pathogenicity of the variant. For these reasons, this variant has been classified as Uncertain Significance. -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 22, 2022	This missense variant replaces proline with arginine at codon 92 of the CHEK2 protein. Computational prediction tools and conservation analyses are inconclusive regarding the impact of this variant on protein structure and function. Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in an individual affected with familial breast cancer (PMID: 23806170). This variant has not been identified 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	Apr 05, 2024	The p.P92R variant (also known as c.275C>G), located in coding exon 1 of the CHEK2 gene, results from a C to G substitution at nucleotide position 275. The proline at codon 92 is replaced by arginine, an amino acid with dissimilar properties. This variant was detected in a 30 year old diagnosed with breast cancer from Pakistan (Rashid MU et al. BMC Cancer, 2013 Jun;13:312). This variant was also detected in a Saudi Arabian patient with sigmoid colon cancer diagnosed at age 49 (AlHarbi M et al. Oncotarget, 2023 Jun;14:580-594). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.050
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.35	T;.;T;T;.;T;.;.;.;.;T;.;.
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.87	.;D;.;.;D;D;D;.;D;D;D;D;D
M_CAP	Benign	0.081	D
MetaRNN	Uncertain	0.57	D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.71	D
MutationAssessor	Uncertain	2.2	M;M;M;M;M;M;M;M;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;N;N
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-2.7	D;D;D;D;D;.;N;D;D;D;D;.;.
REVEL	Uncertain	0.43
Sift	Benign	0.074	T;T;T;T;D;.;D;T;D;D;D;.;.
Sift4G	Benign	0.080	T;T;T;T;T;.;D;T;T;D;D;.;.
Polyphen		0.97	D;D;D;D;D;D;D;D;.;.;.;.;.
Vest4		0.51
MutPred		0.36		Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);Loss of glycosylation at P92 (P = 0.0086);
MVP		0.98
MPC		0.13
ClinPred		0.94	D
GERP RS		5.4
Varity_R		0.22
gMVP		0.52

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: rs779269031; hg19: chr22-29130435;