LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-07-26
Case ID: NM_007194.4_c.1561C_T_20260726_131236
Framework: ACMG/AMP 2015
Variant classification summary

CHEK2  · NP_009125.1:p.(Arg521Trp)  · NM_007194.4
GRCh37: chr22:29083956 G>A  ·  GRCh38: chr22:28687968 G>A
Gene: CHEK2 Transcript: NM_007194.4
Final call
All criteria require review: For research and educational purposes only.
Variant details
Gene
CHEK2
Transcript
NM_007194.4
Protein
NP_009125.1:p.(Arg521Trp)
gnomAD AF
4.511306461819936e-05 (v4.1)
ClinVar
Uncertain significance
OncoKB
Unknown Oncogenic Effect
Classification rationale
Interpretation summary
Generated evidence synthesis
1
NM_007194.4:c.1561C>T (p.Arg521Trp) is a missense variant in CHEK2 altering the nuclear localization signal (NLS) at amino acids 515-522.
2
Functional studies in PMID:37449874 directly tested p.R521W and demonstrated severely impaired nuclear localization using high-content immunofluorescence microscopy in human RPE1 cells. The variant was classified as functionally impaired alongside protein-truncating CHEK2 variants.
3
The ENIGMA CHEK2gether consortium reported that functionally impaired CHEK2 missense variants as a group are associated with moderate breast cancer risk (OR 2.83, 95% CI 2.35-3.41), comparable to the risk of truncating variants.
4
The variant is present in gnomAD at very low frequency: v2.1 AF=0.0053% (14/264,616 alleles) and v4.1 AF=0.0045% (72/1,595,990 alleles), with zero homozygotes and highest subpopulation frequency in East Asians (0.058%).
5
In silico predictors are not supportive of pathogenicity: REVEL=0.205, BayesDel=-0.074, SpliceAI delta=0.00.
6
ClinVar reports this variant as Uncertain Significance with a 1-star review status (15 clinical laboratories), which does not meet the threshold for PP5 or BP6 application.
7
Two moderate pathogenic criteria (PM1 for NLS domain disruption, PS3 for functional evidence of impaired nuclear localization) and one supporting pathogenic criterion (PM2 for rarity in population databases) are met. One supporting benign criterion (BP4 for in silico predictions) is also met.
Final determination:
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 NM_007194.4:c.1561C>T is a missense variant (p.Arg521Trp), not a null variant (nonsense, frameshift, or canonical splice site). The ClinGen SVI PVS1 decision tree (PMC6185798) does not apply to missense substitutions.
pvs1_generic_framework
PS1 Not met No evidence of a different nucleotide change at the same codon previously established as pathogenic. No ClinVar entries reporting a different pathogenic missense change at codon 521.
clinvar pm5_candidates
PS2 Not met No de novo evidence was identified in any of the reviewed publications or ClinVar submissions for this variant.
PS3 Met Functional studies in PMID:37449874 directly tested p.Arg521Trp (R521W) in human RPE1 cells using high-content immunofluorescence microscopy. The variant demonstrated severely impaired nuclear localization, disrupting the nuclear localization signal (NLS) at amino acids 515-522. The authors classified p.R521W as functionally impaired alongside truncating variants and included it in the functionally impaired burden group associated with moderate breast cancer risk (OR 2.83). Kinase activity (KAP1 and CHK2 autophosphorylation assays) was discordant (WT-like/intermediate), but the nuclear mislocalization phenotype was unequivocal and mirrors the effect of protein-truncating CHEK2 variants lacking the NLS.
PMID:37449874
PS4 Not met The variant is present in gnomAD (14/264,616 alleles v2.1; 72/1,595,990 alleles v4.1) at very low frequency but no case-control study has demonstrated statistically significant enrichment of this specific variant in affected individuals versus controls. PMID:37449874 did not report variant-level case counts for p.R521W as it was below the threshold for individual variant analysis.
gnomad_v2 gnomad_v4 PMID:37449874
PS5 Not met No independent observation of a different pathogenic variant at the same codon in an unrelated patient/family. PM5 candidate harvesting found no same-residue pathogenic comparator variants.
pm5_candidates clinvar
PM1 Met The variant p.Arg521Trp is located within the nuclear localization signal (NLS) of CHEK2 at amino acids 515-522, a well-characterized critical functional domain. PMID:37449874 explicitly demonstrated that p.R521W causes severely impaired nuclear localization, phenocopying protein-truncating variants that delete the NLS. The NLS is essential for CHEK2 nuclear import and DNA damage response function.
PMID:37449874
PM2 Met This variant is present in gnomAD at very low frequency: v2.1 AF=5.29e-05 (14/264,616 alleles, 0 homozygotes), v4.1 AF=4.51e-05 (72/1,595,990 alleles, 0 homozygotes). Highest subpopulation frequency is East Asian: v2.1 AF=0.000409 (8/19,552), v4.1 AF=0.000579 (26/44,874). All frequencies are well below the PM2 threshold of 0.1%. grpmax FAF=0.0004053.
gnomad_v2 gnomad_v4
PM5 N/A PM5 candidate harvesting found no same-residue pathogenic comparator variants for codon 521 in CHEK2.
pm5_candidates
PM6 Not met No de novo evidence identified for this variant. The publications reviewed do not report any de novo testing or confirmed de novo occurrence of NM_007194.4:c.1561C>T.
PP1 Not met No cosegregation data available for this variant with disease in families.
PP2 Not met CHEK2 has a substantial number of benign missense variants; missense variation is not a rare/unique mechanism of disease for this gene. PP2 is reserved for genes where missense variants are a common mechanism of disease and benign missense variation is rare.
PMID:37449874
PP3 Not met In silico predictors are not supportive of a pathogenic effect. REVEL score is 0.205 (below the typical pathogenic threshold of 0.5). BayesDel score is -0.074 (benign). SpliceAI max delta is 0.00. Collectively, computational evidence does not support pathogenicity.
revel bayesdel spliceai
PP4 Not met No specific phenotypic data are available for individuals carrying this variant. The publications reviewed do not describe the clinical phenotype of carriers of NM_007194.4:c.1561C>T specifically.
PP5 N/A ClinVar classification is 'Uncertain significance' with review status 'criteria provided, single submitter' (1 star). PP5 requires reputable source (≥3-star expert panel) reporting the variant as pathogenic, per the PP5/BP6 framework rule.
clinvar
BA1 Not met gnomAD allele frequency is far below the BA1 threshold of 1%. v2.1 AF=0.00529%, v4.1 AF=0.00451%, grpmax FAF=0.0405%.
gnomad_v2 gnomad_v4
BS1 Not met Allele frequency is below the BS1 threshold of 0.3%. Highest subpopulation frequency is East Asian: v2.1 AF=0.0409%, v4.1 AF=0.0579%. grpmax FAF=0.0405%. All values are below 0.3%.
gnomad_v2 gnomad_v4
BS2 Not met No homozygotes observed in gnomAD. No evidence of observation in healthy adults in a manner inconsistent with disease penetrance. The variant is too rare to draw conclusions about benign observation.
gnomad_v2 gnomad_v4
BS3 Not met While the kinase activity assays (KAP1 phosphorylation and CHK2 autophosphorylation) in PMID:37449874 showed discordant WT-like/intermediate results — suggesting no major catalytic defect — the variant was nonetheless categorized as functionally impaired by the study due to severely disrupted nuclear localization. The overall functional evidence points toward a damaging effect, not a benign one. BS3 requires well-established functional studies showing no damaging effect.
PMID:37449874
BS4 Not met No segregation data available showing lack of cosegregation with disease.
BP1 Not met BP1 applies to missense variants in genes where only truncating variants cause disease. CHEK2 has both truncating and pathogenic missense variants as demonstrated by PMID:37449874, which identified multiple functionally impaired missense variants with breast cancer risk comparable to truncating variants (OR 2.83).
PMID:37449874
BP2 Not met No observation of this variant in trans with a known pathogenic CHEK2 variant. No data on phase with other variants.
BP4 Met Multiple in silico predictors suggest a benign effect. REVEL score is 0.205, below the typical pathogenic threshold of 0.5. BayesDel score is -0.074, consistent with a benign prediction. SpliceAI delta score is 0.00, predicting no splice impact. HCI prior not applicable (gene not supported). The collective computational evidence favors a benign interpretation.
revel bayesdel spliceai
BP5 Not met No observation of this variant in an individual with an alternate molecular basis for disease (e.g., a known pathogenic variant in another gene explaining the phenotype).
BP6 N/A ClinVar classification is 'Uncertain significance' with review status 'criteria provided, single submitter' (1 star). BP6 requires a reputable source (≥3-star expert panel) reporting the variant as benign/likely benign. The 1-star ClinVar entry reports VUS, not a benign classification.
clinvar
BP3 N/A BP3 applies to in-frame indels in repetitive regions without a known function; this is a missense substitution.
PM3 N/A PM3 applies to recessive disorders where the variant is detected in trans with a pathogenic variant; CHEK2-related cancer predisposition is autosomal dominant.
PM4 N/A PM4 applies to non-frameshift indels causing protein length change; this variant is a missense substitution.
BP7 N/A NM_007194.4:c.1561C>T is a missense variant (p.Arg521Trp), not a synonymous/silent variant. BP7 applies only to synonymous variants with no predicted splice impact.
Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.