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CHEK2
Final classification
Unclassified
CHEK2 c.1604G>A · p.Arg535His
CHEK2

NM_007194.4:c.1604G>A (p.Arg535His) is a missense variant in CHEK2 located in the C-terminal region of the protein, outside the kinase and FHA domains.

Gene
CHEK2
Transcript
NM_007194.4
HGVS · transcript:coding
NM_007194.4:c.1604G>A
Consequence
N/A
exon NC_000022.10
GRCh38
chr22:28687925 C>T
GRCh37
chr22:29083913 C>T
Classification rationale
BP4 Unclassified
CHEK2 c.1604G>A · exon NC_000022.10

NM_007194.4:c.1604G>A (p.Arg535His) is a missense variant in CHEK2 located in the C-terminal region of the protein, outside the kinase and FHA domains.1 Multiple independent computational predictors (REVEL 0.046, BayesDel -0.342, SpliceAI delta 0.00, SIFT Tolerated, Align GVGD C0, MutationTaster Polymorphism) converge on a benign interpretation, satisfying BP4 at supporting benign strength.2 Direct functional assessment in a yeast-based assay (Delimitsou et al. 2019, PMID:30851065) characterized this variant as benign (wild-type-like function), consistent with the computational predictions.3 The variant is present in gnomAD population databases (v2.1: 63/264,906 alleles, AF=0.024%, grpmax FAF=0.16%, 1 homozygote; v4.1: 146/1,594,044 alleles, AF=0.0092%, grpmax FAF=0.11%, 2 homozygotes) with highest frequency in the South Asian subpopulation (0.20% v2.1).4 In ClinVar (VariationID 128067), this variant has received a mixed classification: Likely benign by 8 clinical laboratories, Uncertain significance by 6, and Benign by 1. Review status is single-submitter (1-star) rather than expert panel.5 No pathogenic ACMG/AMP criteria are met. No benign criteria are met beyond BP4 (supporting benign). The evidence is insufficient for a definitive benign classification; the variant remains a variant of uncertain significance (VUS), leaning benign based on computational and functional data.

BP4 Unclassified
1 PMID:30851065
2 revelbayesdelspliceai ↗PMID:30851065
3 PMID:30851065
Gene diagram · NM_007194.4 · variants mapped to exon structure
CHEK2 NM_007194.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 13 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Multiple independent lines of computational evidence predict no damaging effect: REVEL score 0.046 (below the default 0.5 pathogenicity threshold), BayesDel score -0.342 (negative, strongly supporting benign), SpliceAI max delta 0.00 (no predicted splice alteration), and in silico tools from PMID:30851065 (SIFT: Tolerated, Align GVGD: C0, MutationTaster: Polymorphism). Four independent predictors converge on a benign interpretation.
REVEL score 0.046 (threshold for pathogenicity is >0.5)BayesDel score -0.342 (negative scores support benign)SpliceAI max delta 0.00 (no splicing impact)
Assessed · not applied
Pathogenic
PS3 The variant was directly tested in a yeast-based functional assay (PMID:30851065) and categorized as BENIGN (wild-type-like function).
PM1 Residue Arg535 is located in the C-terminal region outside the characterized kinase domain (aa 220-486) and FHA domain (aa 115-175).
PM2 This variant is present in gnomAD v2.1 at a global frequency of 0.024% (63/264,906 alleles, 1 homozygote) and v4.1 at 0.0092% (146/1,594,044 alleles, 2 homozygotes).
PP2 CHEK2 has a high rate of benign missense variation (1.87% missense variants in gnomAD).
PP3 Computational evidence supports a benign interpretation.
PP5 ClinVar classification is 'Likely benign' (8 clinical labs) with 'Uncertain significance' (6 labs) and 'Benign' (1 lab).
Benign
BA1 The highest population allele frequency is 0.20% in the South Asian subpopulation (gnomAD v2.1), which is well below the 1% threshold for BA1.
BS1 The global allele frequency is 0.024% (v2.1) and 0.0092% (v4.1), both below the 0.3% threshold for BS1.
BS2 Only 1 homozygous individual is observed in gnomAD v2.1 (in the South Asian population).
BS3 A single yeast-based functional study (PMID:30851065) characterized this variant as benign.
BP2 No evidence of co-occurrence with a known pathogenic variant in trans for a fully penetrant dominant disorder.
BP5 No evidence that this variant was found in a case with an alternate molecular basis for disease.
BP6 ClinVar review status is 'criteria provided, single submitter' (1-star), not expert panel (3-star) review.
N/A · 11 PVS1 · PS1 · PS2 · PS4 · PM5 · PM6 · PP1 · PP4 · BS4 · BP1 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 9.15909e-05; MAF= 0.00916%, 146/1594044 alleles, homozygotes = 2) and has highest observed frequency in the South Asian population (AF= 0.00130994; MAF= 0.13099%, 119/90844 alleles, homozygotes = 2); grpmax FAF= 0.00111869.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.00023782; MAF= 0.02378%, 63/264906 alleles, homozygotes = 1) and has highest observed frequency in the South Asian population (AF= 0.00201134; MAF= 0.20113%, 61/30328 alleles, homozygotes = 1); grpmax FAF= 0.00160659.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.0004508566275924256, 8/17744 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0092% · 146 / 1,594,044
2 hom · FAF 0.11%
South Asian
119 / 90,844
0.13%
2 hom
Remaining individuals
18 / 62,108
0.029%
Admixed American
2 / 59,840
0.0033%
African/African American
2 / 74,554
0.0027%
European (non-Finnish)
5 / 1,178,590
0.00042%
+ 5 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.024% · 63 / 264,906
1 hom · FAF 0.16%
South Asian
61 / 30,328
0.2%
1 hom
Remaining individuals
1 / 7,038
0.014%
African/African American
1 / 23,358
0.0043%
+ 5 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish))
gnomAD Canada 🇨🇦
0.045% · 8 / 17,744
0 hom · FAF 0.2%
indel · split
South Asian
6 / 1,338
0.45%
Remaining individuals
2 / 1,086
0.18%
+ 7 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, European (non-Finnish))
ClinVar screenshot
ClinVar
In progress — evidence not uploaded yet.
SpliceAI screenshot
In silico
In progress — evidence not uploaded yet.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
In progress — evidence not uploaded yet.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
In progress — evidence not uploaded yet.
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
24879340 ↗ Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
30851065 ↗ Functional characterization of CHEK2 variants in a Saccharomyces cerevisiae system. CLINVAR
34204722 ↗ Prevalence and Clinicopathological Characteristics of Moderate and High-Penetrance Genes in Non-BRCA1/2 Breast Cancer High-Risk Spanish Families. CLINVAR
36315097 ↗ Somatic inactivation of breast cancer predisposition genes in tumors associated with pathogenic germline variants. CLINVAR
37449874 ↗ ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. CLINVAR
15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR