CHEK1 c.484C>T, p.(Arg162Cys)

Reasoning

PM2 is met at supporting strength under the generic non-VCEP fallback. The variant is rare in large reference populations: gnomAD v4.1 overall AF is 0.00125% (20/1,604,350), highest population AF is 0.00450% in East Asians, and joint grpmax FAF is 0.00088%; all are below the generic non-VCEP PM2 threshold of 0.1%. There are no homozygotes. This frequency evidence is compatible with rarity but does not by itself establish CHEK1 disease relevance.

Rule

Generic non-VCEP operating threshold: PM2_supporting applies when the highest reliable population frequency is below 0.1%; a gene/disease-specific VCEP threshold or credible-AF calculation would supersede this fallback.

Evidence considered

• gnomAD v4.1 reports 20/1,604,350 alleles (AF 0.00125%), East Asian AF 0.00450% (2/44,492), joint grpmax FAF 0.00088%, and zero homozygotes.
• gnomAD v2.1 independently reports 3/241,802 alleles (AF 0.00124%), highest observed Admixed American AF 0.00320% (1/31,218), grpmax FAF 0.000298%, and zero homozygotes.
• The gnomAD-Canada query was recorded as unavailable with HTTP 500 rather than as a confirmed absence.

Still missing

• No CHEK1-specific VCEP PM2 threshold or maximum credible allele-frequency calculation based on an established disease, prevalence, penetrance, and allelic heterogeneity is available.
• gnomAD-Canada was unavailable because the recorded query returned HTTP 500; this does not affect the available large gnomAD v2.1/v4.1 evidence.

Sources

Reasoning

PS1 requires an established pathogenic variant with the same amino-acid change (p.(Arg162Cys)) arising from a different nucleotide substitution. No ClinVar record exists for this variant or gene position (ClinVar search returned no result for CHEK1 c.484C>T), and no CSPEC/VCEP framework is available for CHEK1 to supply a curated PS1 comparator list. No other source in the case bundle documents an alternate codon change producing p.(Arg162Cys) with an established pathogenic classification.

Evidence considered

• case_summary.json ClinVar section: 'This variant is absent from ClinVar' with zero variation_ids, so no same-amino-acid comparator classification is available from ClinVar for PS1.

Still missing

• No ClinVar or literature-confirmed pathogenic variant sharing the exact p.(Arg162Cys) amino-acid change was identified in this evidence bundle.

Sources

Reasoning

NM_001274.5:c.484C>T is a missense variant (NP_001265.2:p.(Arg162Cys)). No CHEK1 ClinGen VCEP CSPEC is available for this gene (cspec.found=false, vcep_materials note='no cspec url available'), so the generic ACMG/AMP PP3/BP4 in-silico calibration rule applies, which mandates evaluating exactly ONE mechanism matching the variant's own type. For a missense substitution, only REVEL is used (never SpliceAI, and never BayesDel, which has no verified published calibration for this pipeline). REVEL score = 0.437, which falls within the gray zone [0.250, 0.750] defined by the generic rule, so PP3 is not met. SpliceAI predicts no significant splice impact (max delta = 0.022) but is not the applicable predictor for a missense variant and is not used to satisfy PP3 here.

Rule

generic_acmg_missense_revel_gray_zone

Evidence considered

• REVEL local predictor lookup returned score 0.437 for NM_001274.5:c.484C>T (source_registry key 'revel'), which falls between the generic fallback rule's PP3 threshold (>0.750) and BP4 threshold (<0.250), so neither is met per this lab's REVEL-only missense calibration in generic_acmg_classification_rules.md.
• No CHEK1-specific VCEP CSPEC PP3/BP4 lookup material was found in vcep_materials.json (note: 'no cspec url available'; final_classification_framework.found=false), so the generic ACMG/AMP fallback governs.

Still missing

• No VCEP-specific PP3/BP4 lookup table or CSPEC is available for CHEK1 to override the generic REVEL gray-zone threshold.
• BayesDel score is available (0.181676) but excluded because no verified published calibration/threshold publication is on file for this pipeline.

Sources

Reasoning

The exact variant has no ClinVar record; therefore, no exact-variant pathogenic or likely pathogenic expert-panel assertion is available.

Rule

Apply PP5 only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; do not use laboratory submissions or aggregate labels.

Evidence considered

• ClinVar exact-variant search for NM_001274.5:c.484C>T returned no result.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion would be required.

Sources

Reasoning

BA1 is not met. The highest population-level frequency is gnomAD v4.1 East Asian AF 0.00450% (2/44,492 alleles; grpmax FAF 0.00088%), far below the generic non-VCEP BA1 frequency threshold of 1%. No ancestry-specific frequency approaches that threshold.

Rule

Generic ACMG/AMP fallback: BA1 requires an allele frequency greater than 1%; compare the highest reliable ancestry-stratified frequency and account for sampling uncertainty using FAF where available.

Evidence considered

• No CHEK1 CSPEC/VCEP or local gene-specific framework was retrieved; the case framework specifies generic ACMG/AMP fallback.
• gnomAD v4.1 reports 20/1,604,350 alleles overall (AF 0.00125%), zero homozygotes, East Asian AF 0.00450% (2/44,492), and joint grpmax FAF 0.00088%.
• gnomAD v2.1 reports 3/241,802 alleles overall (AF 0.00124%), zero homozygotes, and Admixed American AF 0.00320% (1/31,218).

Still missing

• No CHEK1-specific VCEP BA1 threshold is available; generic ACMG/AMP fallback was used.

Sources

Reasoning

BS1 is not met. The highest observed ancestry-specific AF is 0.00450% in gnomAD v4.1 East Asians, with grpmax FAF 0.00088%; this is below the generic non-VCEP BS1 threshold of 0.3%. The low frequency does not establish benignity.

Rule

Generic non-VCEP operating threshold: BS1 requires population AF above 0.3%; a disease-specific maximum credible AF would supersede this fallback threshold.

Evidence considered

• gnomAD v4.1 reports a maximum population AF of 0.00450% in East Asians (2/44,492 alleles), overall AF 0.00125%, zero homozygotes, and joint grpmax FAF 0.00088%.
• gnomAD v2.1 reports a maximum population AF of 0.00320% in Admixed Americans (1/31,218 alleles), overall AF 0.00124%, and zero homozygotes.

Still missing

• No CHEK1-specific disease prevalence, penetrance, allelic-heterogeneity, or maximum credible allele-frequency calculation was provided.
• No CHEK1-specific VCEP BS1 threshold is available; generic ACMG/AMP fallback was used.

Sources

Reasoning

Same missense variant and same generic ACMG/AMP fallback calibration as PP3. REVEL score = 0.437 lies within the gray zone [0.250, 0.750] defined for missense variants in generic_acmg_classification_rules.md (BP4 requires REVEL < 0.250), so BP4 is not met. SpliceAI (max delta = 0.022, below the BP4 splice threshold of <0.1) is not applicable because this is a missense variant, not an intronic/synonymous/non-canonical-splice-position variant, and the rule explicitly forbids falling back to the splice-path predictor for a missense variant's own protein-level effect assessment. BayesDel is excluded for lack of a verified published calibration.

Rule

generic_acmg_missense_revel_gray_zone

Evidence considered

• REVEL local predictor lookup returned score 0.437 for NM_001274.5:c.484C>T (source_registry key 'revel'), which falls between the generic fallback rule's PP3 threshold (>0.750) and BP4 threshold (<0.250), so neither is met per this lab's REVEL-only missense calibration in generic_acmg_classification_rules.md.
• SpliceAI max delta score = 0.022 (source_registry key 'spliceai') is well below the BP4 splice threshold of <0.1, but this predictor is not applicable to a missense variant per the generic rule's variant-type matching requirement, so it is not cited as the basis for this BP4 call.

Still missing

• No VCEP-specific PP3/BP4 lookup table or CSPEC is available for CHEK1 to override the generic REVEL gray-zone threshold.
• BayesDel score is available (0.181676) but excluded because no verified published calibration/threshold publication is on file for this pipeline.

Sources

Reasoning

The exact variant has no ClinVar record; therefore, no exact-variant benign or likely benign expert-panel assertion is available.

Rule

Apply BP6 only to an exact-variant ClinVar expert-panel Benign or Likely benign classification; do not use laboratory submissions or aggregate labels.

Evidence considered

• ClinVar exact-variant search for NM_001274.5:c.484C>T returned no result.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign assertion would be required.

Sources

Reasoning

No proband-level parental testing or parentage-confirmment evidence is present in the consolidated case-evidence bundle; de novo occurrence cannot be established.

Rule

Generic ACMG/AMP fallback: PS2 requires a de novo occurrence in an affected individual with maternity and paternity confirmed.

Evidence considered

• No CSPEC/VCEP or local CHEK1-specific framework was retrieved; the case is designated generic_acmg in the review manifest.
• The consolidated evidence bundle contains no proband, parental genotype, parentage, or de novo testing record for CHEK1 c.484C>T (p.Arg162Cys).

Still missing

• Genotype results for the proband and both biological parents, obtained with an appropriate assay.
• Confirmation of biological parentage and clinical phenotype information for the proband.

Reasoning

No CHEK1 ClinGen VCEP specification exists for this case (cspec.found=false, vcep_materials.json note='no cspec url available'), so no PS3-specific assay validation criteria are defined. No variant-specific functional/biochemical assay data for NP_001265.2:p.(Arg162Cys) was located: OncoKB returned no variant-specific reviewed functional evidence ('OncoKB did not identify variant-specific reviewed functional evidence for this variant'), literature_pass.json found zero PMIDs (total_pmids=0), and fulltext_map.json is empty. Two gene-level abstracts identified in prefetch (PMID:38686193, a splicing-truncation case for a different CHEK1 variant c.613+2T>C; PMID:31207404, an siRNA knockdown/HR-repair functional study of CHEK1 as a gene, not this specific missense variant) do not mention or assess R162C/c.484C>T and cannot be used per the strict variant-grounding requirement. No validated kinase activity assay, HR-repair assay, or other functional study of this specific missense substitution was found.

Evidence considered

• prefetch.json OncoKB entry: 'OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up.'
• literature_pass.json: total_pmids=0, note='No PMIDs found across evidence sources.'
• fulltext_map.json is empty ({})
• case_summary.json cspec.found=false; vcep_materials.json note='no cspec url available', framework_mode=generic_acmg_fallback

Still missing

• No CHEK1 VCEP/CSPEC available to define approved functional assay types or PS3 strength calibration
• No variant-specific functional assay (kinase activity, HR repair, cell survival, complementation) reported for p.(Arg162Cys)/c.484C>T
• No full-text literature retrieved mentioning this exact variant in a functional study

Reasoning

No case-control data, affected-case count, control count, or variant-specific enrichment analysis was provided for CHEK1 c.484C>T (p.Arg162Cys).

Rule

Generic ACMG/AMP PS4: prevalence in affected individuals must be significantly increased compared with controls.

Evidence considered

• The consolidated literature pass contains no PMIDs or phenotype/enrichment evidence for this variant.

Still missing

• Obtain a variant-specific case-control study or a well-ascertained case series with appropriate population controls and statistical enrichment analysis.

Reasoning

No CHEK1-specific VCEP/CSPEC was found (review_manifest gene_vcep_dir is null and vcep_materials.json notes 'no cspec url available'), so no curated PM1 hotspot/domain boundary definition is available. The cancerhotspots.org lookup for CHEK1 R162 explicitly returned no statistically significant hotspot ('This variant does not lie in a statistically significant hotspot'), and no domain-level benign-variation-depletion data (e.g., missense constraint mapped to the kinase domain) is present in the bundle to support a generic-ACMG PM1 call.

Evidence considered

• evidence.json hotspots result: cancerhotspots.org search for 'CHEK1 R162' returned search_status 'no_result' / found=false, with evidence_sentence 'This variant does not lie in a statistically significant hotspot.'
• OncoKB gene-level summary notes CHEK1 is 'an intracellular kinase' but provides no variant-specific or domain-boundary functional data for R162 (not_reviewed=true, is_variant_specific=false).

Still missing

• No CHEK1 VCEP/CSPEC-defined critical domain or hotspot boundary is available.
• cancerhotspots.org lookup for CHEK1 R162 returned no significant hotspot result.
• No regional missense constraint / benign-variation-depletion data for the CHEK1 kinase domain is present in this evidence bundle.

Sources

Reasoning

No affected-proband observation identifies NM_001274.5:c.484C>T (p.Arg162Cys) with a pathogenic or likely pathogenic CHEK1 variant in trans. No phased genotype, parental testing, or recessive CHEK1 disease model was provided; therefore PM3 cannot be assessed.

Rule

Generic ACMG/AMP PM3: require the variant to be observed in trans with a pathogenic/likely pathogenic variant in an affected individual for a recessive disorder.

Evidence considered

• No CHEK1 CSPEC/VCEP material was available, so generic ACMG/AMP evidence semantics are the applicable fallback.
• The case bundle reports no exact ClinVar record or publication for the assessed variant and provides no affected-proband, second-allele, or phase data.

Still missing

• Affected-proband genotype(s) containing the assessed variant and a second CHEK1 variant.
• Classification evidence for any second CHEK1 variant and direct phase evidence (parental segregation or validated read-based phasing).
• Established recessive CHEK1 disease context applicable to the proband phenotype.

Sources

Reasoning

The case's dedicated pm5_candidates artifact explicitly declined automated same-residue candidate harvesting ('Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting'), reporting pm5_mode 'unknown', eligible_for_classic_pm5_search=false, and same_residue_candidates=0. No manual ClinVar or literature search for alternate pathogenic missense changes at codon 162 was independently performed within the scope of this evidence bundle (ClinVar overall search for this gene/position returned no result).

Evidence considered

• pm5_candidates_summary in prefetch data: pm5_mode='unknown', eligible_for_classic_pm5_search=false, same_residue_candidates=0, with hermes_instruction to not apply PM5 from this artifact alone.
• ClinVar returned no result for this gene/variant search, providing no leads to alternate same-residue pathogenic missense variants.

Still missing

• pm5_candidates.json harvesting was explicitly skipped; no verified same-residue alternate-amino-acid pathogenic comparator has been confirmed or excluded.
• A manual ClinVar/literature search specifically for other missense changes at CHEK1 codon 162 (e.g., p.Arg162His, p.Arg162Ser) has not been performed within this bundle.

Sources

Reasoning

No proband-level parental testing result is present. A presumed de novo occurrence cannot be determined.

Rule

Generic ACMG/AMP fallback: PM6 requires a de novo occurrence in an affected individual when maternity and paternity are not confirmed.

Evidence considered

• No CSPEC/VCEP or local CHEK1-specific framework was retrieved; the case is designated generic_acmg in the review manifest.
• The consolidated evidence bundle contains no proband or parental genotype data and no statement of presumed de novo occurrence for CHEK1 c.484C>T (p.Arg162Cys).

Still missing

• Genotype results for the proband and parents, or documentation that parental samples are unavailable together with evidence that the variant is de novo by clinical testing.
• Proband phenotype and family-history information relevant to the suspected CHEK1-associated condition.

Reasoning

No family segregation data, affected-relative genotypes, unaffected-relative genotypes, or informative meioses are present in the consolidated case-evidence bundle.

Rule

Generic ACMG/AMP fallback: PP1 requires co-segregation of the variant with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No CSPEC/VCEP or local CHEK1-specific framework was retrieved; the case is designated generic_acmg in the review manifest.
• The consolidated evidence bundle contains no family-level genotype-phenotype segregation data or meiosis count for CHEK1 c.484C>T (p.Arg162Cys).

Still missing

• Pedigree with phenotype, age, and genotype information for informative relatives.
• Number of independent informative meioses and evidence that the variant co-segregates with the relevant phenotype.

Reasoning

PP2 requires establishing that missense variants are a common mechanism of disease in CHEK1 and that benign missense variants are uncommon. No CHEK1-specific VCEP/CSPEC guidance on missense mechanism is available (gene_vcep_dir null, vcep_materials.json empty). The only germline-mechanism literature retrieved for this gene (e.g., the c.613+2T>C splicing/truncation case report) documents a loss-of-function/truncating mechanism rather than establishing missense as a common pathogenic mechanism, and no gnomAD missense constraint (Z-score) or ClinVar missense pathogenic-vs-benign ratio data for CHEK1 is present in this bundle.

Evidence considered

• OncoKB gene summary describes CHEK1 as 'an intracellular kinase... overexpressed in various solid and hematologic malignancies' but gives no missense-specific mechanism statement and is explicitly not_reviewed/not variant-specific.
• Case pvs1_gene_context literature search (PMID:38686193) documents a germline CHEK1 splice-site variant causing truncation at the kinase domain classified as loss-of-function, illustrating a truncating rather than missense disease mechanism for this gene in the retrieved literature.

Still missing

• No gnomAD missense constraint metric (missense Z-score/o:e ratio) for CHEK1 is present in the evidence bundle.
• No ClinVar-derived missense pathogenic:benign ratio for CHEK1 is available to establish whether benign missense variants are uncommon.
• Retrieved germline literature for CHEK1 documents a truncating/splicing LOF mechanism rather than a missense mechanism, which does not resolve whether missense is 'commonly' pathogenic in this gene.

Sources

Reasoning

No proband phenotype, clinical indication, or evidence that the phenotype is highly specific for a CHEK1-associated condition was provided.

Rule

Generic ACMG/AMP PP4: the patient's phenotype or family history must be highly specific for a disease with a single genetic etiology.

Evidence considered

• No phenotype-specific case information or variant literature was present in the consolidated evidence bundle.

Still missing

• Provide the proband phenotype and clinical assessment, together with evidence that the phenotype is highly specific for a CHEK1-associated disease mechanism.

Reasoning

BS2 is not assessed. gnomAD v2.1 and v4.1 report no homozygotes, and the bundle provides no phenotype-confirmed healthy adult carriers or disease-specific penetrance data. Sparse heterozygous population observations alone do not demonstrate observation in healthy adults incompatible with disease.

Rule

Generic ACMG/AMP BS2 requires observation in a healthy adult individual for a disorder expected to be fully penetrant at an early age; unphenotyped aggregate reference-population counts are insufficient by themselves.

Evidence considered

• gnomAD v4.1 reports 20 alleles among 1,604,350 alleles and zero homozygotes.
• gnomAD v2.1 reports 3 alleles among 241,802 alleles and zero homozygotes.
• The provided population sources do not provide age or phenotype data for individual carriers.

Still missing

• Phenotype- and age-ascertained observations of carriers in healthy adults are needed.
• CHEK1 disease validity, inheritance model, and penetrance data are needed to judge whether unaffected adult carriers would be informative.

Sources

Reasoning

Same evidentiary gap as PS3: no CHEK1 VCEP/CSPEC exists to define validated benign-range assay controls or BS3 strength calibration, and no variant-specific functional assay data (normal/wild-type-equivalent kinase activity, HR repair proficiency, etc.) for p.(Arg162Cys)/c.484C>T was located in any source. No evidence of a negative/normal functional assay result for this specific variant.

Evidence considered

• prefetch.json OncoKB entry: 'OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up.'
• literature_pass.json: total_pmids=0, note='No PMIDs found across evidence sources.'
• fulltext_map.json is empty ({})
• case_summary.json cspec.found=false; vcep_materials.json note='no cspec url available', framework_mode=generic_acmg_fallback

Still missing

• No CHEK1 VCEP/CSPEC available to define approved functional assay types or BS3 strength calibration
• No variant-specific functional assay showing normal/wild-type activity reported for p.(Arg162Cys)/c.484C>T
• No full-text literature retrieved mentioning this exact variant in a functional study

Reasoning

No convincing non-segregation observations are present: the bundle provides no genotype-positive unaffected relatives, genotype-negative affected relatives, or other informative familial discordance data.

Rule

Generic ACMG/AMP fallback: BS4 requires lack of segregation in affected members of a family; it should be applied only when familial data are sufficiently informative.

Evidence considered

• No CSPEC/VCEP or local CHEK1-specific framework was retrieved; the case is designated generic_acmg in the review manifest.
• The consolidated evidence bundle contains no family observations demonstrating non-segregation for CHEK1 c.484C>T (p.Arg162Cys).

Still missing

• Pedigree, genotype, phenotype, and age-at-evaluation data for informative relatives.
• Evidence of robust non-segregation after accounting for age-related penetrance, phenocopies, and the relevant inheritance model.

Reasoning

BP1 requires establishing that missense variants are not a common cause of disease in this gene (i.e., disease is predominantly caused by other variant types). While the sole germline-disease literature identified for CHEK1 in this bundle describes a truncating/loss-of-function splice variant as the disease-causing mechanism (consistent with a gene where truncating variants predominate), no CHEK1-specific VCEP/CSPEC statement on missense mechanism, and no quantitative missense-vs-truncating pathogenic variant ratio (e.g., from ClinVar or a curated gene-specific framework), is available in this bundle to confirm BP1 applicability with confidence.

Evidence considered

• pvs1_gene_context literature search (PMID:38686193) documents a germline CHEK1 splice-site variant causing kinase-domain truncation and loss-of-function, the only germline disease-mechanism evidence in this bundle, suggesting a truncating-predominant mechanism but not itself a quantitative missense-rarity statement needed to confirm BP1.

Still missing

• No CHEK1 VCEP/CSPEC statement on missense-vs-truncating disease mechanism is available.
• No quantitative ClinVar missense-vs-truncating pathogenic variant ratio for CHEK1 is present in this bundle to confirm that missense variants are not a common disease mechanism.

Reasoning

No observation places NM_001274.5:c.484C>T (p.Arg162Cys) in cis with a pathogenic or likely pathogenic CHEK1 variant, nor in trans with one in a disease setting for which CHEK1 is established as dominant. No phase or affected/unaffected phenotype data were provided; therefore BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2: require a qualifying observed co-occurrence with a pathogenic/likely pathogenic variant, interpreted with phase and disease inheritance mode.

Evidence considered

• No CHEK1 CSPEC/VCEP material was available, so generic ACMG/AMP evidence semantics are the applicable fallback.
• The case bundle reports no exact ClinVar record or publication for the assessed variant and provides no co-occurrence, phase, or pedigree data.

Still missing

• A co-occurring pathogenic/likely pathogenic CHEK1 variant in the same individual.
• Direct phase evidence demonstrating cis or trans configuration.
• Phenotype and inheritance information establishing whether the relevant CHEK1 disease mechanism is dominant or recessive.

Sources

Reasoning

No affected individual data or alternate molecular diagnosis was provided to establish that this variant was found in a case with another molecular basis for disease.

Rule

Generic ACMG/AMP BP5: the variant is found in a case with an alternate molecular basis for disease.

Evidence considered

• The consolidated evidence bundle contains no proband-level molecular diagnostic information.

Still missing

• Provide a phenotypically affected individual with a definitive alternate molecular diagnosis sufficient to explain the clinical presentation.