22-28704723-T-C

Variant names:

• chr22-28704723-T-C
• rs1547014
• NM_007194.4:c.847-1157A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007194.4(CHEK2):​c.847-1157A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,012 control chromosomes in the GnomAD database, including 33,006 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (33006 hom., cov: 32)
• Consequence: CHEK2 NM_007194.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 42 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007194.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHEK2	NM_007194.4	MANE Select	c.847-1157A>G		intron	N/A	NP_009125.1
	CHEK2	NM_001005735.3		c.976-1157A>G		intron	N/A	NP_001005735.1
	CHEK2	NM_001438293.1		c.940-1157A>G		intron	N/A	NP_001425222.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHEK2	ENST00000404276.6	TSL:1 MANE Select	c.847-1157A>G		intron	N/A	ENSP00000385747.1
	CHEK2	ENST00000382580.6	TSL:1	c.976-1157A>G		intron	N/A	ENSP00000372023.2
	CHEK2	ENST00000402731.6	TSL:1	c.646-1157A>G		intron	N/A	ENSP00000384835.2

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98717 AN: 151896 Hom.: 32991 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.669

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.650 AC: 98776 AN: 152012 Hom.: 33006 Cov.: 32 AF XY: 0.656 AC XY: 48721 AN XY: 74302

African (AFR) AF: 0.502 AC: 20802 AN: 41426

American (AMR) AF: 0.628 AC: 9586 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2719 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4365 AN: 5170

South Asian (SAS) AF: 0.831 AC: 4005 AN: 4822

European-Finnish (FIN) AF: 0.734 AC: 7759 AN: 10570

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47284 AN: 67984

Other (OTH) AF: 0.668 AC: 1410 AN: 2112

Alfa AF: 0.689 Hom.: 169697

Bravo AF: 0.634

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.56
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1547014; hg19: chr22-29100711; COSMIC: COSV60415611;