22-28734401-A-T

Variant names:

• chr22-28734401-A-T
• rs587782401
• NM_007194.4:c.319+2T>A

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 16P and 1B. PVS1 PP5_Very_Strong BS2_Supporting

The NM_007194.4(CHEK2):​c.319+2T>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.0000465 in 1,613,644 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000085 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000042 (0 hom.)
• Consequence: CHEK2 NM_007194.4 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:17
• Conservation: PhyloP100: 5.92
• Publications: 28 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 15 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP5: Variant 22-28734401-A-T is Pathogenic according to our data. Variant chr22-28734401-A-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 142352.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAd4 at 13 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.319+2T>A		splice_donor_variant, intron_variant	Intron 2 of 14	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.319+2T>A		splice_donor_variant, intron_variant	Intron 2 of 14	1	NM_007194.4	ENSP00000385747.1

Frequencies

GnomAD3 genomes AF: 0.0000854 AC: 13 AN: 152224 Hom.: 0 Cov.: 31

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: 0.000376

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000678 AC: 17 AN: 250830 AF XY: 0.0000663

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000555

Gnomad NFE exome AF: 0.0000441

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000424 AC: 62 AN: 1461420 Hom.: 0 Cov.: 33 AF XY: 0.0000413 AC XY: 30 AN XY: 727020

African (AFR) AF: 0.00 AC: 0 AN: 33474

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.000824 AC: 44 AN: 53400

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000135 AC: 15 AN: 1111612

Other (OTH) AF: 0.0000497 AC: 3 AN: 60358

GnomAD4 genome AF: 0.0000854 AC: 13 AN: 152224 Hom.: 0 Cov.: 31 AF XY: 0.0000941 AC XY: 7 AN XY: 74366

African (AFR) AF: 0.00 AC: 0 AN: 41476

American (AMR) AF: 0.00 AC: 0 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

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

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

European-Finnish (FIN) AF: 0.000376 AC: 4 AN: 10626

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

European-Non Finnish (NFE) AF: 0.000132 AC: 9 AN: 68034

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.000327 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000576 AC: 7

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

May 01, 2020

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 20, 2019

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 27, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 20, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant disrupts a canonical splice-donor site and interferes with normal CHEK2 mRNA splicing. In the published literature, the variant has been reported in individuals with breast and/or ovarian cancer(PMIDs: 31882575 (2019), 30333958 (2018), 28608266 (2017), 26681312 (2015)), and in an individual with colorectal cancer (PMID: 27696107 (2016)). Based on the available information, this variant is classified as likely pathogenic. -

Nov 30, 2020

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Observed in individuals with CHEK2-related cancers (Mantere 2017, Rohlin 2017, Brovkina 2018, Dominguez-Valentin 2018, Olkinuora 2018); Case control studies, in the Finnish population, suggest this variant is associated with breast cancer (Nurmi 2019); Not observed at a significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 31948886, 31882575, 30927251, 30333958, 30573798, 27751358, 27696107, 28386063, 24713400, 28608266, 26681312, 23960188) -

Familial cancer of breast Pathogenic:6

Aug 21, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 26, 2022

BRCAlab, Lund University

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 09, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. -

Jul 02, 2018

Mendelics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 21, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 2 of the CHEK2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and is likely to result in the loss of the initiator methionine. This variant is present in population databases (rs587782401, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with thyroid cancer, colorectal cancer, prostate cancer, and breast and/or ovarian cancer (PMID: 26681312, 27696107, 28608266, 30333958, 30927251, 31882575, 31948886, 35980532, 36551643, 38201513). ClinVar contains an entry for this variant (Variation ID: 142352). Studies have shown that disruption of this splice site results in skipping of exon 2, and is expected to result in the loss of the initiator methionine (PMID: 37725924; internal data). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Jan 10, 2018

Counsyl

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Mar 02, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.319+2T>A pathogenic intronic mutation results from a T to A substitution two nucleotides after coding exon 1 in the CHEK2 gene. The alteration has previously been reported in an individual diagnosed with a microsatellite-stable colorectal cancer at age 76 years (Rohlin A et al. Fam. Cancer 2017 Apr;16(2):195-203) and in another individual diagnosed with thyroid cancer and bilateral breast cancer who also had a family history of breast, thyroid, and endometrial cancers (Dominguez-Valentin M et al. Fam. Cancer 2018 Jan;17(1):141-153).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. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this alteration is interpreted as a disease-causing mutation. -

Nov 17, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a T>A nucleotide substitution at the +2 position of intron 2 of the CHEK2 gene. Computational splicing tools predict that this variant may have a significant impact on RNA splicing. RNA studies have been reported that this variant results in the skipping of exon 2 and the removal of the translation start codon (PMID: 37725924, ClinVar: SCV000633168.9). This variant has been reported in individuals affected with breast cancer (PMID: 26681312, 28608266, 30333958, 31882575, 33471991, 35314380, 36551643). This variant has been identified in 29/282228 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of CHEK2 function is a known mechanism of disease. Based on available evidence, this variant is classified as Likely Pathogenic. -

Breast cancer, susceptibility to;C3469524:Prostate cancer susceptibility Pathogenic:1

Dec 31, 2019

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This c.319+2T>A variant in CHEK2 gene affects 5’ splice site of intron 2. The variant is expected to disrupt normal splicing of CHEK2 mRNA, leading to an absent or abnormal protein product. This variant has been reported in multiple unrelated individuals with breast, colorectal and thyroid cancers (PMID: 28386063, 27696107, 28608266). It is present in 29/282228 alleles in the gnomAD population database. Based on the currently available information, the CHEK2 c.319+2T>A variant has been classified as likely pathogenic. -

Familial cancer of breast;C0376358:Prostate cancer;C0585442:Bone osteosarcoma;C5882668:CHEK2-related cancer predisposition Pathogenic:1

May 18, 2017

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Malignant tumor of breast Pathogenic:1

Dec 04, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CHEK2 c.319+2T>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 5' splicing donor site. A recent report confirmed this prediction, by demonstrating that the variant didn't produce any full length transcripts in a splicing reporter minigene assay (Sanoguera-Miralles_2023). The variant allele was found at a frequency of 0.0001 in 282,228 control chromosomes (gnomAD v2.1), however in some subpopulations e.g. in the Finnish and Estonian the variant was reported with much higher frequencies, i.e. 0.0006 and 0.0019 respectively. These subpopulation frequencies are higher than the estimated maximum expected for a pathogenic variant in CHEK2 causing Breast Cancer phenotype (0.00031). The variant has been reported in patients with breast cancer and other tumor phenotypes, including e.g. microsatellite-stable colorectal cancer and Cowden-like syndrome (e.g. de Miranda_2013, Susswein_2015, Leedom_2016, Rohlin_2016, Dominguez-Valentin_2017). In a large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 20/60,466 cases, and 7/53,461 controls (Dorling_2021, reported through LOVD). A case control study in the Finnish population, suggested that this variant is associated with elevated risk of breast cancer (Nurmi_2022). While another case-control study performed in Estonians showed that the relative frequency of the variant in the in the general population is 0.09%, and in variant carriers most breast cancer cases were diagnosed after the age of 50y (Pavlovica_2022). The following publications have been ascertained in the context of this evaluation (PMID: 23960188, 26681312, 27696107, 28608266, 27751358, 33471991, 35314380, 36551643, 37725924). 13 other submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic (n=3) or likely pathogenic (n=10). Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Pathogenic	0.31
CADD	Pathogenic	33
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.93
FATHMM_MKL	Uncertain	0.97	D
PhyloP100		5.9
GERP RS		5.3
PromoterAI		-0.14	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
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: rs587782401; hg19: chr22-29130389;