NM_007194.4:c.542G>A

CHEK2 · NP_009125.1:p.(Arg181His) · NM_007194.4

GRCh37: chr22:29121015 C>T · GRCh38: chr22:28725027 C>T

Gene: CHEK2 Transcript: NM_007194.4

Final call

Likely Benign

BS3 supporting BP4 supporting BP6 supporting

Variant details

Gene

CHEK2

Transcript

NM_007194.4

Protein

NP_009125.1:p.(Arg181His)

gnomAD AF

5.2666341994158375e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_007194.4:c.542G>A (p.Arg181His) in CHEK2 is present in gnomAD at low frequency (v2.1 AF=0.0127%, v4.1 AF=0.0053%) with one homozygote observed in the East Asian population.

In a well-established cell-based functional assay (KAP1 phosphorylation in RPE1-CHEK2-KO cells), p.Arg181His was classified as NEUTRAL, retaining >50% of wild-type CHK2 kinase activity (Kleiblova et al. 2019).

Multiple lines of in silico evidence suggest no damaging impact: SpliceAI predicts no splicing alteration (max delta=0.00), BayesDel score is in the benign range (-0.032), and REVEL is borderline (0.46).

ClinVar aggregate classification is Likely benign from 10 clinical diagnostic laboratories, with an additional 8 labs reporting Uncertain significance (Variation ID 5598).

The variant has been reported in 1/400 sporadic prostate cancer cases (Dong et al. 2003), 1/516 familial breast cancer patients (Dufault et al. 2004), and 2/1928 breast/ovarian cancer patients (Kleiblova et al. 2019) without statistically significant enrichment versus controls.

No de novo observations, co-segregation data, or statistically significant case-control enrichment have been reported for this variant.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Benign classification because either one strong benign criterion plus one supporting benign criterion, or at least two supporting benign criteria, are present.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 does not apply to missense variants. NM_007194.4:c.542G>A is a missense substitution (p.Arg181His), not a null variant (nonsense, frameshift, or canonical ±1,2 splice site). Generic PVS1 framework (PMC6185798) confirms variant bucket is 'other' with no canonical splice consensus disruption.	pvs1_generic_framework
PS1	Not met	No different nucleotide change at codon 181 producing the same missense change (p.Arg181His) has been established as pathogenic. There is no evidence that c.542G>C or c.542G>T (also producing p.Arg181His) has been classified as pathogenic.
PS2	Not met	No de novo observations have been reported for this variant in public databases or the literature. PS2 requires a confirmed de novo occurrence with both maternity and paternity confirmed.
PS3	Not met	PS3 requires well-established functional studies showing a damaging effect. In Kleiblova et al. (PMID:31050813), a validated cell-based functional assay (KAP1 phosphorylation in RPE1-CHEK2-KO cells) classified c.542G>A (p.Arg181His) as NEUTRAL, with CHK2 kinase activity retained at >50% of wild-type. This contradicts a damaging interpretation. An exploratory search referenced Boonen et al. (2022, PMID:35654782) as showing a loss-of-function effect, but this source was not verified with full-text and remains unconfirmed.	PMID:31050813
PS4	Not met	PS4 requires statistically significant enrichment of the variant in affected individuals versus controls. Dong et al. (PMID:12533788) found c.542G>A in 1/400 sporadic prostate cancer cases and 0/423 controls. Dufault et al. (PMID:15095295) found it in 1/516 familial breast cancer patients and 0/500 controls (p=0.38, not significant). Kleiblova et al. (PMID:31050813) found it in 2/1928 patients and 0/3360 population-matched controls. None reached statistical significance. Insufficient proband counts for PS4.	PMID:12533788 PMID:15095295 PMID:31050813
PS5	Not met	PS5 requires a different pathogenic variant at the same amino acid position. The only alternate missense at codon 181 is c.541C>T (p.Arg181Cys). This variant has not been established as pathogenic — it is classified as VUS/neutral in functional studies (Kleiblova et al. 2019 classified it as NEUTRAL; Wu et al. 2006 showed only partially reduced kinase activity).	PMID:31050813 PMID:16835864
PM1	Not met	PM1 requires location in a mutational hot spot or critical functional domain with absent or very low benign variation. While codon 181 lies within the FHA domain (important for CHK2 dimerization and activation), functional studies demonstrate that missense variants at this position (p.Arg181His, p.Arg181Cys) are tolerated (classified as NEUTRAL by Kleiblova et al. 2019). The CHEK2 VCEP criteria.json contains no structured PM1 domain specification. Given functional neutrality, PM1 is not supported.	PMID:31050813
PM2	Not met	PM2 applies when a variant is absent from population databases. This variant is present in gnomAD: v2.1 AF=0.0001273 (36/282788 alleles, 1 homozygote), v4.1 AF=5.27×10⁻⁵ (85/1613934 alleles, 1 homozygote). While the overall frequency is low (<0.1%), the variant is not absent. The presence of a homozygote in the East Asian population (v2.1, v4.1) indicates the variant is tolerated in a healthy adult, further weakening any PM2 argument.	gnomad_v2 gnomad_v4
PM5	N/A	No same-residue comparator variants with pathogenic classification were identified. PM5 candidate harvesting returned no valid comparators.
PM6	Not met	PM6 requires a de novo observation with maternity and paternity confirmed. No de novo reports have been identified for this variant.
PP1	Not met	PP1 requires co-segregation of the variant with disease in multiple affected family members. No co-segregation data are available for this variant in the literature.
PP2	Not met	PP2 requires a missense variant in a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease. CHEK2 has a high rate of benign missense variation, exemplified by the common p.I157T variant observed at ~3% population frequency with no significant cancer risk elevation. PP2 is not applicable.	gnomad_v2 gnomad_v4
PP3	Not met	PP3 requires multiple lines of in silico evidence supporting a deleterious effect. REVEL score is 0.46 (borderline, below typical pathogenic threshold of ~0.7). BayesDel score is -0.032 (benign range). SpliceAI max delta is 0.00 (no splicing impact). HCI prior is not available. The in silico evidence is mixed and does not converge on a damaging prediction. PP3 is not met.	revel bayesdel spliceai
PP4	Not met	PP4 requires the patient's phenotype or family history to be highly specific for the gene. No individual-level phenotype data are available for carriers of this variant beyond aggregate counts in case series.
PP5	Not met	PP5 requires a reputable source to have classified the variant as pathogenic. ClinVar aggregate classification for Variation ID 5598 is Likely benign (9 labs), Uncertain significance (8 labs), with 1 additional likely benign and 1 benign. No reputable source has classified this variant as pathogenic; the predominant clinical consensus is benign/likely benign.	clinvar
BA1	Not met	BA1 requires allele frequency >1% in a population database. The highest observed population frequency is 0.125% in East Asian (gnomAD v2.1), well below the 1% threshold. Overall AF is 0.0127% (v2.1) and 0.0053% (v4.1). BA1 is not met.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires allele frequency >0.3% in a population database. The highest observed population frequency is 0.125% in East Asian (gnomAD v2.1), below the 0.3% threshold. BS1 is not met.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age. CHEK2-related cancer predisposition is an autosomal dominant condition with moderate penetrance and adult onset; it does not exhibit full penetrance at an early age. While the variant is observed in gnomAD (including 1 homozygote), the BS2 criterion is not satisfied under the standard ACMG/AMP interpretation due to incomplete penetrance and late onset of CHEK2-associated cancers.	gnomad_v2 gnomad_v4
BS3	Met	BS3 is met at supporting level. Kleiblova et al. (PMID:31050813) performed a well-established cell-based functional assay quantifying CHK2-specific phosphorylation of endogenous KAP1 in human non-transformed RPE1-CHEK2-knock-out cells. The c.542G>A (p.Arg181His) variant was classified as NEUTRAL, retaining >50% of wild-type CHK2 kinase activity. This assay is considered well-validated — it reflects in vivo CHK2 behavior more accurately than in vitro kinase assays, resolves discrepancies seen in prior yeast-based and overexpression systems, and correctly stratified known pathogenic and benign controls. The neutral functional classification provides supporting evidence for a benign effect.	PMID:31050813
BS4	Not met	BS4 requires lack of segregation of the variant with disease in affected family members. No segregation studies are available for this variant. Dufault et al. (PMID:15095295) reported the variant in 1/516 familial breast cancer patients and 0/500 controls (p=0.38), but this is case-control frequency data, not segregation analysis. BS4 is not met.
BP1	N/A	BP1 applies when a missense variant occurs in a gene where only truncating variants cause disease. CHEK2 has known pathogenic missense variants (e.g., p.Arg117Gly, p.Arg145Trp, p.Gly167Arg in the FHA domain; p.Thr367Metfs in kinase domain from c.1100delC is truncating but missense variants in the kinase domain are also pathogenic). BP1 is not applicable.
BP2	N/A	BP2 applies when a variant is observed in trans with a pathogenic variant for a recessive disorder, or in cis with a pathogenic variant in any inheritance pattern. CHEK2 is an autosomal dominant cancer predisposition gene; BP2 observation in trans with a recessive disorder is not the relevant disease mechanism. Not applicable.
BP4	Met	BP4 is met at supporting level. Multiple lines of in silico evidence suggest no impact on gene product: SpliceAI predicts no splicing alteration (max delta = 0.00); BayesDel score is -0.032 (benign range, below zero); REVEL score is 0.46, which is borderline and does not reach the typical pathogenic threshold (~0.7). The convergence of SpliceAI and BayesDel on a benign prediction, with REVEL being non-contributory, satisfies BP4 at the supporting level.	revel bayesdel spliceai
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such case has been reported for this variant. Kleiblova et al. (PMID:31050813) noted that carriers in their cohort included one with a coincident BRCA1 mutation, but this was a single observation and the classification as BP5 would require systematic exclusion of CHEK2 contribution.
BP6	Met	BP6 is met at supporting level. The ClinVar aggregate classification for Variation ID 5598 is Likely benign, reported by 10 clinical diagnostic laboratories (9 as Likely benign, 1 as Benign). An additional 8 submissions classify it as Uncertain significance and 1 as likely benign. The plurality of clinical laboratories with assertion criteria favor a benign interpretation. No expert panel review has been performed.	clinvar
BP7	N/A	BP7 applies only to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. NM_007194.4:c.542G>A is a missense variant (p.Arg181His), not synonymous. BP7 is not applicable.

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