Classification rationale

PM2 BP4 VUS

CHEK1 c.965G>A

This variant (NM_001274.5:c.965G>A, p.Arg322His) is a missense substitution in CHEK1, a gene with limited but emerging evidence for germline loss-of-function disease association. No CSPEC or VCEP framework exists for CHEK1; assessment follows generic ACMG/AMP 2015 guidelines.¹ The variant is observed at extremely low frequency in gnomAD population databases (v2.1 AF=0.004%, v4.1 AF=0.002%), meeting the PM2 criterion at supporting strength.² Multiple in silico predictors unanimously suggest a neutral effect: REVEL score 0.055, BayesDel score -0.267, and SpliceAI max delta 0.03, meeting BP4 at supporting_benign strength.³ ClinVar reports this variant as Uncertain significance (VCV2397701, criteria provided, single submitter: Ambry Genetics). There are no reputable sources classifying this variant as pathogenic or benign.⁴ No variant-specific functional studies, de novo observations, segregation data, or case-control enrichment data were identified in the available literature or databases.⁵ The final evidence profile includes one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4). These cancel, resulting in a classification of Uncertain significance per the ACMG/AMP 2015 combination rules.⁶

PM2 + BP4 → VUS

1 pvs1_gene_contextfinal_classification_framework

2 gnomad_v2 ↗gnomad_v4 ↗

3 revelbayesdelspliceai ↗

4 clinvar ↗

5 oncokb ↗

6 generic_acmg_combination_rules

Gene diagram · NM_001274.5 · variants mapped to exon structure

CHEK1 NM_001274.5

Fetching transcript structure from UCSC…

Applied criteria · 2 applied · 20 assessed

Applied · 2

Strength Supporting Moderate Strong Very strong

✓

PM2 supporting Pathogenic

This variant is present at extremely low frequency in gnomAD population databases: v2.1 overall AF=0.004% (10/251,222 alleles, 0 homozygotes) and v4.1 overall AF=0.002% (36/1,613,908 alleles, 0 homozygotes), both well below the 0.1% PM2 threshold. Maximum subpopulation frequency is 0.0275% (South Asian, v4.1). Downgraded to supporting strength given the variant is not completely absent and the limited germline disease association of CHEK1.

gnomAD v2.1: AF=3.98e-05 (10/251222 alleles)grpmax FAF=8.53e-05

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

✓

BP4 supporting Benign

Multiple lines of computational evidence predict no damaging effect: REVEL score 0.055 (well below the 0.29 benign threshold), BayesDel score -0.267 (negative, indicating benign), and SpliceAI max delta 0.03 (no predicted splice impact). Three independent in silico tools unanimously predict a neutral/benign effect.

REVEL: 0.055 (benign rangebelow 0.29 threshold)BayesDel: -0.267 (negative score

spliceai ↗

Assessed · not applied

Pathogenic

PS1 No evidence identified of a different nucleotide change at codon 322 producing the same p.Arg322His substitution that has been classified as pathogenic.

PS2 No de novo occurrence data available for this variant.

PS3 No variant-specific or systematically characterized range functional data identified for CHEK1 p.Arg322His.

PS4 No case-control data or statistically significant enrichment data available comparing prevalence of this variant in affected individuals versus general population controls.

PM1 Position p.Arg322 lies in the SQ/TQ cluster domain (SCD) of CHEK1, a regulatory region involved in checkpoint signaling.

PM6 No de novo occurrence data available for this variant.

PP1 No co-segregation data with disease in multiple affected family members is available for this variant.

PP2 CHEK1 has not been established as a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease.

PP3 Multiple lines of computational evidence predict a benign effect: REVEL score 0.055 (well below pathogenic threshold), BayesDel score -0.267 (negative, benign-leaning), and SpliceAI max delta 0.03 (no predicted splice impact).

PP4 No patient phenotype or family history data are available to assess whether the phenotype is highly specific for a disease with a single genetic etiology.

PP5 ClinVar classification for this variant is Uncertain significance (1-star, single submitter: Ambry Genetics), not Pathogenic.

Benign

BA1 Maximum population allele frequency in gnomAD is 0.0275% (South Asian, v4.1), well below the 1% BA1 threshold.

BS1 Maximum population allele frequency in gnomAD is 0.0275% (South Asian, v4.1), well below the 0.3% BS1 threshold.

BS2 No evidence that this variant has been observed in a healthy adult individual for a fully penetrant disorder with a recessive or dominant inheritance pattern relevant to CHEK1.

BS3 No well-established in vitro or in vivo functional studies demonstrate a neutral effect for CHEK1 p.Arg322His.

BS4 No segregation data available to assess lack of co-segregation with disease in affected family members.

BP1 Although loss-of-function is supported as a disease mechanism for CHEK1 (based on germline literature review), CHEK1 has not been established as a gene where ONLY truncating variants cause disease.

BP2 No data available on whether this variant has been observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern.

BP5 No evidence that this variant has been observed in a case where an alternate molecular basis for disease was identified.

BP6 ClinVar classification for this variant is Uncertain significance (1-star, single submitter), not Benign or Likely Benign.

N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 2.23061e-05; MAF= 0.00223%, 36/1613908 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000274701; MAF= 0.02747%, 25/91008 alleles, homozygotes = 0); grpmax FAF= 0.00019002.

v2.1

This variant is present in gnomAD v2.1 (AF= 3.98054e-05; MAF= 0.00398%, 10/251222 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000196477; MAF= 0.01965%, 6/30538 alleles, homozygotes = 0); grpmax FAF= 8.528e-05.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

0.0022% · 36 / 1,613,908
0 hom · FAF 0.019%

South Asian 25 / 91,008	0.027%
African/African American 2 / 74,994	0.0027%
Admixed American 1 / 59,958	0.0017%
European (non-Finnish) 8 / 1,179,988	0.00068%

+ 6 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)

gnomAD v2.1

0.004% · 10 / 251,222
0 hom · FAF 0.0085%

South Asian 6 / 30,538	0.02%
East Asian 1 / 18,378	0.0054%
Admixed American 1 / 34,512	0.0029%
European (non-Finnish) 2 / 113,680	0.0018%

+ 4 not observed (African/African American, Ashkenazi Jewish, European (Finnish), Remaining individuals)

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 2397701)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.055. BayesDel score = -0.266804.

SpliceAI ↗

Functional Unknown Oncogenic Effect

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CHEK1, an intracellular kinase, is overexpressed in various solid and hematologic malignancies.

OncoKB ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Sources & reference links

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots