22-28734401-A-T

Position:

• chr22-28734401-A-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

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

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 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 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 [Likely_pathogenic]. Clinvar id is 142352.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-28734401-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.319+2T>A		splice_donor_variant, intron_variant		ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.319+2T>A		splice_donor_variant, intron_variant		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

GnomAD3 exomes AF: 0.0000678 AC: 17 AN: 250830 Hom.: 0 AF XY: 0.0000663 AC XY: 9 AN XY: 135658

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 SAS 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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000824

Gnomad4 NFE exome AF: 0.0000135

Gnomad4 OTH exome AF: 0.0000497

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

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000376

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.00

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

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 30, 2020	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 20, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 20, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	May 27, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2020	- -

Familial cancer of breast Pathogenic:6

Likely pathogenic, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Aug 26, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 21, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	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). 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 (Invitae). 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 09, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Jan 10, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 02, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 21, 2022	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. To our knowledge, functional RNA studies have not been reported for this variant. This variant has been reported in individuals affected with breast cancer and ovarian cancer (PMID: 26681312, 28608266, 30333958, 31882575) and in an individual who was referred for clinical familial adenomatous polyposis- and/or Lynch syndrome mutation analyses (PMID: 27696107). In the Finnish population where this variant has been identified in 15/25102 chromosomes, this variant is associated with elevated risk of breast cancer (PMID: 30927251). 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

Likely pathogenic, criteria provided, single submitter

clinical testing

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Dec 31, 2019

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:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C5882668:Li-Fraumeni syndrome 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 18, 2017

- -

Malignant tumor of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Dec 04, 2023

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
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8

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

Publications

LitVar

Other links and lift over

dbSNP: rs587782401; hg19: chr22-29130389;