22-28725241-A-T

Variant names:

• chr22-28725241-A-T
• rs560596101
• NM_007194.4:c.444+2T>A

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_007194.4(CHEK2):​c.444+2T>A variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CHEK2 NM_007194.4 splice_donor, intron
• Scores: Splicing: ADA: 0.9993
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.10
• Publications: 3 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: Pathogenic. The variant received 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 9, offset of 4, new splice context is: aagGTaatg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 22-28725241-A-T is Pathogenic according to our data. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-28725241-A-T is described in CliVar as Likely_pathogenic. Clinvar id is 3266953.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.444+2T>A		splice_donor_variant, intron_variant	Intron 3 of 14	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.444+2T>A		splice_donor_variant, intron_variant	Intron 3 of 14	1	NM_007194.4	ENSP00000385747.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 152170 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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 32

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 152170 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74326

African (AFR) AF: 0.00 AC: 0 AN: 41460

American (AMR) AF: 0.00 AC: 0 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68030

Other (OTH) AF: 0.00 AC: 0 AN: 2092

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Apr 22, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.444+2T>A intronic variant results from a T to A substitution two nucleotides after coding exon 2 in the CHEK2 gene. This variant has been reported in a cohort of individuals undergoing multi-gene panel testing for hereditary cancer (Sutcliffe EG et al. Cancer Genet, 2020 Aug;246-247:12-17). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.037	T
BayesDel_noAF	Benign	-0.18
CADD	Pathogenic	35
DANN	Benign	0.80
Eigen	Pathogenic	0.68
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.94	D
PhyloP100		7.1
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=1/99	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Benign	0.59
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.95		Position offset: -2
DS_DL_spliceai		1.0		Position offset: 2

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

Other links and lift over

dbSNP: rs560596101; hg19: chr22-29121229;