22-28734727-C-T

Position:

• chr22-28734727-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The ENST00000404276.6(CHEK2):​c.-6G>A variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000893 in 1,612,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00060 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000036 (0 hom.)
• Consequence: CHEK2 ENST00000404276.6 splice_region, 5_prime_UTR
• Scores: Splicing: ADA: 0.9803
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4 B:6
• Conservation: PhyloP100: 3.17

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 Likely_benign. Variant got -1 ACMG points.

• BP6: Variant 22-28734727-C-T is Benign according to our data. Variant chr22-28734727-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 128041.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=4, Likely_benign=3}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.-6G>A		splice_region_variant, 5_prime_UTR_variant	2/15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.-6G>A		splice_region_variant, 5_prime_UTR_variant	2/15	1	NM_007194.4	ENSP00000385747	P2

Frequencies

GnomAD3 genomes AF: 0.000594 AC: 90 AN: 151398 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00216

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000659

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

GnomAD3 exomes AF: 0.000131 AC: 32 AN: 244186 Hom.: 0 AF XY: 0.0000906 AC XY: 12 AN XY: 132454

Gnomad AFR exome AF: 0.00201

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: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000363 AC: 53 AN: 1461144 Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23 AN XY: 726842

Gnomad4 AFR exome AF: 0.00143

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.000601 AC: 91 AN: 151514 Hom.: 0 Cov.: 31 AF XY: 0.000717 AC XY: 53 AN XY: 73968

Gnomad4 AFR AF: 0.00218

Gnomad4 AMR AF: 0.0000658

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000293 Hom.: 0

Bravo AF: 0.000654

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:4 Benign:6

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial cancer of breast Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	May 08, 2023	This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk. -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Aug 03, 2016	- -

not provided Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 15, 2024	Nucleotide is not conserved across species and the substitution has no predicted effect on splicing; Published functional studies demonstrate no damaging effect: produced transcripts similar to wildtype in a minigene assay (PMID: 37725924); Observed in individuals with breast, colon, and other cancers (PMID: 25186627, 27534895, 27978560, 35534704); Alters the Kozak sequence, which plays a major role in the initiation of translation; This variant is associated with the following publications: (PMID: 27534895, 25186627, 27978560, 14687034, 3313277, 35534704, 37725924) -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 28, 2023	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 05, 2021	Variant summary: CHEK2 c.-6G>A is located in the untranslated mRNA region upstream of the initiation codon. Although this region is indicated to be affected by pseudogene interference, a BLAT search for the reference sequence (TTTTGAGgTCGTGATGTCTCGGGAGTCGGA, i.e. a 25 or 30 nucleotide sequence surrounding the location of the variant) gave no hits on other chromosomes/regions. The variant allele was found at a frequency of 0.00013 in 244186 control chromosomes, predominantly at a frequency of 0.002 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 6.4 fold of the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (0.00031), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. c.-6G>A has been reported in the literature in an African American female patient affected with breast cancer (Tung 2014) and in an MMR-proficient colon cancer patient (race not specified) (Pearlman 2016), however the variant was also reported to be found in 4/2559 African American women, who are older than age 70 years, and who have never had cancer (in the FLOSSIES database). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (likely benign, n=1; VUS, n=3). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the absence of any evidence supporting an actionable outcome as outlined above, the variant was classified as benign. -

Familial cancer of breast;C0346629:Colorectal cancer;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C5882668:Li-Fraumeni syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Jul 07, 2022

This variant has been reported in the literature in 1 individual with breast cancer and 1 individual with MMR-proficient colorectal cancer (Tung 2015 PMID:25186627; Pearlman 2017 PMID:27978560). This variant is present in the Genome Aggregation Database (Highest reported MAF: 0.2% [89/41178]; https://gnomad.broadinstitute.org/variant/22-28734727-C-T?dataset=gnomad_r3), and in ClinVar, with classifications ranging benign to uncertain significance (Variation ID:128041). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is located 6 nucleotides upstream from the initiation codon in the conserved Kozak sequence, which is critical for initiation of translation. However, it is unclear what effect this variant may have. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -

CHEK2-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 06, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Malignant tumor of breast Benign:1

Likely benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The CHEK2 c.-6G>A variant was identified in 2 of 5216 proband chromosomes (frequency: 0.0004) from individuals with breast and colon cancer and was present in 5 of 19,768 control chromosomes (frequency: 0.0003) from healthy individuals (Tung 2015, Pearlman 2017). The variant was also identified in dbSNP (rs376995740) as “with other allele”, in ClinVar (classified as "likely benign" by Color and Integrated Genetics and "uncertain significance" by GeneDx and Counsyl). The variant was identified in control databases in 53 of 269,654 chromosomes at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 53 of 23,662 chromosomes (freq: 0.00224), but not in the “Other”, Latino, European, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The variant lies 6 base pairs upstream of the ATG start site and is part of the Kozak consensus sequences which is important for translation initiation, although a G is generally present at the -6 position it is known to vary at this position. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -

Hereditary cancer-predisposing syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Feb 16, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
DANN	Benign	0.90
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.98
dbscSNV1_RF	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs376995740; hg19: chr22-29130715;