CHEK2 c.1561C>T, p.(Arg521Trp)

Reasoning

BP1 is a supporting benign criterion that applies to a missense variant in a gene for which primarily truncating variants are known to cause disease (Richards et al. 2015, PMID:25741868). The variant under assessment, NM_007194.4:c.1561C>T (p.Arg521Trp), is a missense substitution (consequence class 'missense'). CHEK2 is a gene in which disease-causing alleles are predominantly protein-truncating/loss-of-function: PMID:18163131 states that 'In CHEK2, ATM, BRIP1 and PALB2, most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay' with only a small proportion being rare missense variants, and the CHEK2 literature consistently centres on the truncating founder allele c.1100delC. This supports BP1 at supporting strength. A modest caveat is that functionally impaired missense alleles have been reported to confer some risk (PMID:37449874, OR 2.83 for the aggregate impaired group), so missense is not entirely excluded from the mechanism; this does not overturn the predominantly truncating mechanism but is recorded for transparency. The governing CHEK2 CSPEC (doc 522546466) supplied no extractable BP1 rule or calibrated strength, so the generic ACMG/AMP 2015 BP1 (supporting) was applied.

Rule

BP1 (supporting) applies to a missense variant in a gene where primarily truncating variants cause disease; CHEK2 is such a gene (Richards et al. 2015).

Evidence considered

• BP1 (Richards et al. 2015, PMID:25741868) applies to a missense variant in a gene where primarily truncating variants cause disease; assessed at the criterion's default supporting strength.
• Consequence class for NM_007194.4:c.1561C>T is missense (NP_009125.1:p.(Arg521Trp)), the variant class BP1 is scoped to.
• PMID:18163131: 'In CHEK2, ATM, BRIP1 and PALB2, most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay through nonsense codons or translational frameshifts. A small proportion is likely to be rare missense variants that disrupt critical functions.' This directly supports a predominantly truncating disease mechanism for CHEK2.
• PMID:37449874 notes functionally impaired CHEK2 missense variants were associated with a moderate breast cancer risk (OR 2.83, 95% CI 2.35-3.41) comparable to truncating variants for the aggregate impaired group, a caveat indicating missense is not entirely excluded from the disease mechanism.

Still missing

• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable BP1 rule or calibrated strength, so the generic ACMG/AMP 2015 BP1 (supporting) definition was used.

Sources

Reasoning

NM_007194.4:c.1561C>T encodes the missense substitution NP_009125.1:p.(Arg521Trp) in CHEK2 exon 15, so BP4 is evaluated on the REVEL protein-impact path. The local REVEL score is 0.205, which is at or below the ClinGen SVI supporting BP4 threshold of <=0.29 (Pejaver et al. 2022, PMID:36413997), so BP4 is met at supporting strength. It does not reach moderate (<=0.183) or strong (<=0.016). The SpliceAI result (max delta 0.006) is numerically benign-direction but is out of scope for a missense variant and was not used as BP4 support. BayesDel (-0.0743) was disregarded because no generic ACMG-strength calibration is established. The governing CHEK2 VCEP specification (CSPEC doc 522546466) contains no gene-specific BP4 computational rule, so the generic ClinGen SVI REVEL calibration applies.

Rule

Missense variant: BP4 requires REVEL <= 0.29 (supporting), <= 0.183 (moderate), or <= 0.016 (strong), per ClinGen SVI REVEL calibration (PMID:36413997).

Evidence considered

• Missense consequence (NM_007194.4:c.1561C>T, NP_009125.1:p.(Arg521Trp), CHEK2 exon 15) selects the REVEL path for BP4; the SpliceAI path does not apply.
• Local REVEL score for this variant is 0.205 (source: local REVEL v1.3 lookup, chrom 22 GRCh38 position 28687968 G>A).
• REVEL 0.205 is at or below the ClinGen SVI supporting BP4 threshold of <=0.29 but above the moderate <=0.183 cutoff, giving supporting-strength BP4 only (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997).
• SpliceAI max delta score 0.006 is not valid BP4 support for a missense variant and was not used.
• BayesDel score -0.0743 was disregarded: no generic ACMG-strength BayesDel calibration exists and the CHEK2 VCEP specifies no cutpoint.
• The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification for CHEK2 v1.0 (CSPEC doc 522546466) provides no structured gene-specific computational rule, so the generic ClinGen SVI REVEL calibration is applied.

Sources

Reasoning

PS1 requires that a different nucleotide change encoding the SAME amino-acid change has been established as pathogenic, i.e. that a variant producing p.Arg521Trp is a known pathogenic allele (Richards et al. 2015, PMID:25741868). The only ClinVar record for CHEK2 NM_007194.4:c.1561C>T (ClinVarID 140881) is this exact variant, and it is classified Uncertain significance by all submitters (16 clinical laboratories; review status 'criteria provided, multiple submitters, no conflicts', no expert-panel submission, no pathogenic assertion). No alternative nucleotide substitution encoding p.Arg521Trp is reported as pathogenic, and the automated same-residue comparator harvest (pm5_candidates.json) returned no established-pathogenic codon-521 alleles. PS1's prerequisite - a previously established pathogenic variant with the identical amino-acid change - is therefore absent. The governing ClinGen HBOP CHEK2 v1.0 CSPEC (doc 522546466) is present but yielded no extractable PS1 rule text (framework_complete=false, empty rule payload), so the generic ACMG/AMP 2015 PS1 definition was applied.

Rule

PS1 requires the same amino-acid change as a previously established pathogenic variant; the only p.Arg521Trp record is a VUS, so PS1 is not met (Richards et al. 2015).

Evidence considered

• PS1 (Richards et al. 2015, PMID:25741868) is met when the same amino-acid change as a previously established pathogenic variant is present, regardless of the nucleotide change; the gene-agnostic ACMG/AMP 2015 definition was applied because the CHEK2 CSPEC provided no PS1 ruleset.
• ClinVar (ClinVarID 140881) holds NM_007194.4(CHEK2):c.1561C>T (p.Arg521Trp) as Uncertain significance with 16 clinical laboratories submitting, review status 'criteria provided, multiple submitters, no conflicts' and zero expert-panel submissions; the record itself is the same amino-acid change under assessment and is not pathogenic.
• pm5_candidates.json reports 0 same-residue candidate alleles and 0 expert-panel P/LP candidates at CHEK2 codon 521 (pm5_mode 'unknown', eligible_for_classic_pm5_search=false), so no established pathogenic variant at the same residue with the identical amino-acid change was available.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466; case framework source cspec_ruleset, framework_complete=false, empty rule_payload) contained no extractable PS1 specification.

Still missing

• No established pathogenic variant carrying the identical p.Arg521Trp amino-acid change was identified in ClinVar or in the literature consulted.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable PS1 rule or gene-specific same-amino-acid-list, so PS1 was assessed with the generic ACMG/AMP 2015 definition.

Sources

Reasoning

PS3 requires well-established functional studies demonstrating a damaging effect on the gene or gene product (Richards et al. 2015, PMID:25741868). Three independent functional datasets address CHEK2 NM_007194.4:c.1561C>T (p.Arg521Trp) and they do not converge on a damaging effect. PMID:37449874 (ENIGMA CHEK2gether) included p.R521W among 102 variants categorized as functionally impaired, but this classification rests on severely aberrant nuclear localization (intense cytoplasmic positivity resembling c.1100delC mislocalization); the same study states the codon-521 variants scored WT/intermediate in its KAP1 and CHK2 kinase assays, i.e. kinase function was not convincingly lost. PMID:34903604 placed p.R521W among nine missense variants with an intermediate defect in CHK2-mediated KAP1 p.S473 phosphorylation in a mouse-ES complementation assay, a readout between functional and clearly damaging. PMID:30851065 tested p.(Arg521Trp) in an in vivo yeast MMS-growth assay with a WT positive control and the non-functional c.1100delC negative control and categorized it benign, growth comparable to wild type. Because no single well-established assay demonstrates a clearly damaging effect and one validated assay reads as wild-type-like, the ACMG requirement for PS3 is not satisfied at any strength. The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) is present but yielded no extractable PS3/BS3 functional-assay specification (framework_complete=false, empty rule payload), so the generic ACMG/AMP 2015 PS3 definition was applied and no VCEP-calibrated functional strength was available.

Rule

PS3 requires well-established functional studies showing a damaging effect; conflicting benign, intermediate, and localization-based impaired results do not meet the criterion (Richards et al. 2015).

Evidence considered

• PS3 (Richards et al. 2015, PMID:25741868) is met when well-established functional studies show a damaging effect on the gene or gene product; the gene-agnostic ACMG/AMP 2015 definition was applied because the CHEK2 CSPEC provided no functional-assay ruleset.
• PMID:37449874 (ENIGMA CHEK2gether, 430 CHEK2 missense VUS in hTERT-RPE1 CHEK2-knockout cells; KAP1-pS473 and CHK2-S516 kinase assays plus nuclear-to-cytoplasmic localization): p.R521W was included among the 102 functionally impaired variants. Direct quote: "Among the 102 functionally impaired variants, we also included two variants, p.R521W and p.R521Q (scored WT/intermediate and intermediate/WT in kinase assays, respectively), which were the only analyzed missense variants with severely impaired nuclear localization (Fig. 3B)." The impairment therefore derives from mislocalization, while the kinase assays scored WT/intermediate rather than clearly damaging.
• PMID:34903604 (mouse embryonic stem-cell complementation assay; CHK2-mediated KAP1 p.S473 phosphorylation after 10 Gy IR, FACS readout, 50 CHEK2 missense VUS): p.R521W was one of nine variants with an INTERMEDIATE functional defect, i.e. between functional/synonymous and strongly damaging truncating-like variants, not a clear damaging effect.
• PMID:30851065 (in vivo yeast S. cerevisiae MMS-growth assay, RAD53/SML1-deleted strain; WT positive control, c.1100delC negative control; 120 CHEK2 missense variants): p.(Arg521Trp) was categorized benign, growth comparable to wild type rather than to the non-functional c.1100delC control; benign categorization used normalized median >0.70 and normalized standardized difference of means >0.30.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466; cross-referenced in the case framework as source cspec_ruleset, framework_complete=false, empty rule_payload) contained no extractable PS3/BS3 functional-assay specification; its transcript of record is ENST00000404276.6.

Still missing

• Functional results for p.Arg521Trp are discordant across assays (yeast benign by MMS growth, mouse-ES intermediate KAP1 phosphorylation, ENIGMA impaired nuclear localization but WT/intermediate kinase); no single well-established assay demonstrates a clearly damaging effect.
• The two PMIDs flagged as PS3 leads by the literature triage (32980694, 33309985) have no fetched full text or paper_extracts entry in this case and could not be consulted.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable PS3/BS3 functional-assay rules, so no VCEP-calibrated functional strength could be applied.

Sources

Reasoning

PS4 requires that the prevalence of this exact variant be significantly increased in affected individuals compared with controls (variant-level case-control enrichment). The only case-control evidence available is the ENIGMA CHEK2gether burden analysis (PMID:37449874): across 73,048 breast cancer cases and 88,658 controls the odds ratio rose with functional category to 2.83 (95% CI 2.35-3.41) for the aggregate class of 'functionally impaired' CHEK2 missense variants. That is a class-level estimate, not a variant-specific one: p.Arg521Trp was not individually tested (the study only tested variants with >=10 carriers) and no per-variant odds ratio is reported. p.Arg521Trp was assigned to the impaired class because of severely aberrant nuclear localization, despite WT/intermediate CHK2 kinase assay scores, so even the class membership for this variant rests on a non-case-control assay. No other retrieved source reports case-control counts for this exact variant. A class-level OR is not variant-specific evidence, so PS4 is not met. The ClinGen HBOP CHEK2 V1.0 specification exists but its criteria payload could not be retrieved, so it is unverified whether that VCEP would permit a class-based PS4; flagged for human review.

Rule

ACMG/AMP 2015 PS4: significantly increased prevalence of the variant in affected individuals compared with controls (variant-level case-control enrichment).

Evidence considered

• ENIGMA CHEK2gether (PMID:37449874): burden case-control analysis of 73,048 breast cancer cases and 88,658 controls; ORs increased across functional categories to 2.83 (95% CI 2.35-3.41) for functionally impaired missense variants. This is a class-level estimate; per-variant case-control risk for p.Arg521Trp is not separately reported (only variants with >=10 carriers were individually tested).
• p.Arg521Trp was included in the functionally impaired class as one of two codon-521 variants (with p.Arg521Q) that showed severely impaired nuclear localization; both had WT/intermediate or intermediate/WT kinase assay scores, so class membership for this variant derives from a localization assay rather than a variant-specific case-control observation.
• ACMG/AMP 2015 (PMID:25741868) defines PS4 as significantly increased prevalence of the variant in affected versus control individuals; generic ACMG provides no numeric threshold for PS4.
• No numeric comparison was applied for PS4 because no published or VCEP-specific numeric PS4 threshold was available in the governing sources.

Still missing

• No variant-specific case-control odds ratio is available; p.Arg521Trp was not individually tested in PMID:37449874 (only variants with >=10 carriers were).
• The governing ClinGen HBOP CHEK2 V1.0 specification criteria could not be retrieved (empty/unstructured ruleset), so any VCEP-specific PS4 rule, class-based PS4 allowance, or numeric threshold is unverified.

Sources

Reasoning

PM1 requires the variant to lie in a mutational hot spot and/or a critical and well-established functional domain without benign variation (Richards et al. 2015, PMID:25741868). Two routes were checked. (1) Hot spot: the CancerHotspots query for CHEK2 R521 returned no statistically significant hotspot row (found=false, 'This variant does not lie in a statistically significant hotspot'). (2) Critical functional domain: the authoritative VCEP domain list for this gene was consulted first - vcep_materials.json domain_tables is empty for CHEK2 ({}), and the governing ClinGen HBOP CHEK2 v1.0 CSPEC (doc 522546466) is an unstructured ruleset with framework_complete=false and an empty rule payload, so there is no VCEP-approved critical-domain table against which residue 521 can be matched. Independently, residue 521 lies within the CHEK2 nuclear localization signal (NLS) spanning residues 515-522 (PMID:37449874), and codon-521 substitutions are the only analyzed missense variants with severely impaired nuclear localization; this makes the NLS a functionally important region, but it is not an established ACMG/AMP 'critical and well-established functional domain' for CHEK2 in the absence of a VCEP specification, and the 'without benign variation' condition cannot be satisfied or excluded here (no gene-level benign-missense-constraint metric is available and this variant itself is present in gnomAD at a low but non-zero frequency, 14/264616 alleles, AF 5.29e-5). PM1 is therefore not met under the generic definition. Human review is flagged because the domain_table channel that would authoritatively settle the NLS/kinase-domain question was unavailable in this case.

Rule

PM1 requires a mutational hot spot or a critical and well-established functional domain without benign variation; no hotspot was found and no VCEP-approved critical-domain list exists for CHEK2 (Richards et al. 2015).

Evidence considered

• PM1 (Richards et al. 2015, PMID:25741868) is met when the variant is in a mutational hot spot and/or critical and well-established functional domain without benign variation; the generic definition was applied because no CHEK2 VCEP-domain specification was extractable.
• vcep_materials.json (and the case framework it mirrors) carries an empty domain_tables object for CHEK2, so the authoritative per-gene approved critical-domain list could not be consulted; the governing CSPEC is ClinGen HBOP CHEK2 v1.0, doc 522546466, framework_mode=unstructured_ruleset, framework_complete=false, rule_payload={}.
• CancerHotspots/OncoKB hotspot query for CHEK2 R521 returned found=false ('This variant does not lie in a statistically significant hotspot'; record_id 'CHEK2 R521', source_data {}); no source_registry key exists for this resource, so it is recorded here as prose only.
• PMID:37449874 reports that the CHEK2 nuclear localization signal spans amino acids 515-522 and that only codon-521 alterations (p.R521W, p.R521Q) showed severely impaired nuclear localization with intense cytoplasmic positivity resembling c.1100delC mislocalization, indicating functional importance of this region.
• gnomAD v2.1 (source gnomad_v2) shows the variant is present at 14/264616 alleles (AF 5.29e-5, grpmax FAF 2.21e-4), a low but non-zero population frequency relevant to the 'without benign variation' condition of PM1.

Still missing

• vcep_materials.json domain_tables is empty for CHEK2 and the ClinGen HBOP CHEK2 v1.0 CSPEC ruleset is unstructured (framework_complete=false, empty rule_payload), so no VCEP-approved critical functional domain list was available to check residue 521 against.
• Residue 521 sits in the CHEK2 nuclear localization signal (residues 515-522; PMID:37449874), but no governing specification establishes the NLS as an ACMG-critical domain, and benign-variation status at this residue could not be excluded from the available data.

Sources

Reasoning

PM2 (supporting) is applied when a variant is absent or extremely rare in population databases; the operative metric is the highest ancestry-specific filtering allele frequency (the gnomAD grpmax/popmax FAF), and the generic supporting threshold supplied here is <=0.0001. Although the overall (global) AF is below that threshold in every dataset (gnomAD v2.1 5.29069e-05, 14/264,616; v4.1 4.51131e-05, 72/1,595,990), the grpmax FAF exceeds it wherever exomes contribute: gnomAD v2.1 grpmax FAF 0.00022085 and gnomAD v4.1 grpmax FAF 0.0004053, both driven by East Asian enrichment (East Asian AF 0.000409165 in v2.1, 19,552 alleles; 0.0005794 in v4.1, 44,874 alleles; the Korean subpopulation reaches 0.00131 in v2.1). The gnomAD v2.1 non-cancer exome subset independently reproduces this enrichment (AF 4.95594e-05, 11/221,956; grpmax FAF 0.00018708; East Asian AF 0.00036726, 7/19,060), so it is not merely a cancer-cohort or tumour-panel artifact. Homozygote count is 0 throughout. Because the popmax FAF exceeds 0.0001 in the exome-inclusive and all-comers datasets, PM2 is not met; treating the sub-threshold global AF as decisive would be a threshold artifact that ignores real ancestry-specific commonality. (The gnomAD v3.1 genomes-only non-cancer set shows a lower grpmax FAF of 1.171e-05, but it is genome-only, orders of magnitude smaller for the relevant East Asian signal, and its nominal popmax rests on a single 1KG:JPT allele at N=204.)

Rule

PM2 met if popmax (grpmax) filtering allele frequency <= 0.0001 (ClinGen SVI supporting; PMID:25741868)

Evidence considered

• gnomAD v2.1 (all-comers): total AF 5.29069e-05 (14/264,616 alleles), 0 homozygotes; grpmax (popmax) FAF 0.00022085; highest ancestry group East Asian AF 0.000409165 (8/19,552); Korean subpopulation AF 0.00131 (5/3,814).
• gnomAD v4.1 (all-comers): total AF 4.51131e-05 (72/1,595,990 alleles), 0 homozygotes; grpmax FAF 0.0004053; highest ancestry group East Asian AF 0.0005794 (26/44,874).
• gnomAD v2.1 non-cancer exomes: AF 4.95594e-05 (11/221,956 alleles), 0 homozygotes; grpmax FAF 0.00018708; East Asian AF 0.00036726 (7/19,060) - the same East Asian enrichment is present after removing cancer cohorts, arguing against a cohort artifact.
• gnomAD v3.1 non-cancer genomes: AF 3.38016e-05 (5/147,922 alleles), 0 homozygotes; grpmax FAF 1.171e-05 (genome-only, no exome cohort in v3).
• PM2 assessed on the grpmax/popmax filtering allele frequency against the supplied generic supporting threshold of <=0.0001 (ClinGen SVI PM2 downgrade to supporting; PMID:25741868); the popmax FAF exceeds 0.0001 in both all-comers datasets and in the v2.1 non-cancer exome subset.
• Per task guidance the all-comers GNOMAD_V2_1/GNOMAD_V4_1 totals were treated as the default because no VCEP-mandated non-cancer/exome-only source could be confirmed; the non-cancer subsets were inspected and yield the same PM2 conclusion.

Still missing

• The CHEK2 VCEP v1.0 (cspec doc 522546466) population criteria were not machine-readable in this case (framework extracted as unstructured_ruleset with an empty rule_payload), so the VCEP-specific PM2 threshold and its prescribed population source could not be confirmed. Generic ACMG/ClinGen-SVI defaults were applied; if the VCEP sets a different popmax FAF threshold or mandates a specific subset, the PM2 call should be re-checked.

Sources

Reasoning

PM5 requires a missense change at an amino-acid residue where a DIFFERENT missense change has been determined to be pathogenic (Richards et al. 2015, PMID:25741868). The residue under assessment is CHEK2 codon 521 (reference Arg). The automated same-residue comparator harvest (pm5_candidates.json) found 0 same-residue candidates, 0 expert-panel P/LP candidates and 0 non-expert-majority P/LP candidates, and explicitly declined to apply PM5 from that artifact alone (pm5_mode 'unknown', eligible_for_classic_pm5_search=false). ClinVar holds no established pathogenic (expert-panel or majority P/LP) missense variant at CHEK2 codon 521; the only codon-521 records are the VUS under assessment and its neighbours. The literature names a second codon-521 allele, p.Arg521Gln (R521Q), but PMID:37449874 reports it only as functionally impaired in a research assay (alongside p.R521W), which is not an established pathogenic classification and therefore does not satisfy PM5's requirement for a pathogenic comparator. PM5 is not met. The governing CHEK2 CSPEC (doc 522546466) supplied no extractable PM5 rule, so the generic ACMG/AMP 2015 definition was applied.

Rule

PM5 requires a different pathogenic missense at the same residue; no such pathogenic codon-521 comparator exists (Richards et al. 2015).

Evidence considered

• PM5 (Richards et al. 2015, PMID:25741868) is met when a different missense change at the same residue has been determined to be pathogenic; the gene-agnostic ACMG/AMP 2015 definition was applied because the CHEK2 CSPEC provided no PM5 ruleset.
• pm5_candidates.json: residue 521 (reference R, observed W), 0 total candidates seen, 0 same-residue candidates, 0 expert-panel P/LP candidates, 0 non-expert-majority P/LP candidates; recommendation level 'not_applicable' with an instruction not to apply PM5 from the artifact alone.
• ClinVar (ClinVarID 140881) contains no established pathogenic or expert-panel missense comparator at codon 521; the record for the variant under assessment is Uncertain significance.
• PMID:37449874 names p.Arg521Gln (R521Q) as a second codon-521 allele alongside p.R521W, but reports it only as functionally impaired in a research assay (WT/intermediate kinase score, impaired nuclear localization), not as a clinically established pathogenic variant.

Still missing

• No ClinVar-classified pathogenic missense comparator at CHEK2 codon 521 was found; the automated comparator harvest (pm5_candidates.json) was disabled (eligible_for_classic_pm5_search=false) and returned zero candidates.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable PM5 rule, so the generic ACMG/AMP 2015 definition was used.

Sources

Reasoning

PP2 is a supporting benign criterion that requires BOTH that the gene has a low rate of benign missense variation AND that missense variants are a common mechanism of disease (Richards et al. 2015, PMID:25741868). The second condition clearly fails for CHEK2. PMID:18163131 states that in CHEK2 (as in ATM, BRIP1 and PALB2) 'most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay through nonsense codons or translational frameshifts' and that only 'a small proportion is likely to be rare missense variants that disrupt critical functions.' CHEK2 disease predisposition is therefore driven predominantly by protein-truncating/loss-of-function alleles, and missense variation is a minority mechanism, not a common one. In addition, no gene-level benign-missense constraint metric (e.g. a missense Z-score / benign-missense rate) was supplied in this case, so the first PP2 condition could not be positively established. With at least one PP2 precondition failing, PP2 is not met. The governing CHEK2 CSPEC (doc 522546466) supplied no extractable PP2 rule, so the generic ACMG/AMP 2015 definition was applied.

Rule

PP2 requires low benign missense variation AND missense as a common disease mechanism; CHEK2 disease is predominantly truncating, so PP2 is not met (Richards et al. 2015).

Evidence considered

• PP2 (Richards et al. 2015, PMID:25741868) is met only if missense variation is a common mechanism of disease in a gene with a low rate of benign missense variation; the generic definition was applied because the CHEK2 CSPEC provided no PP2 ruleset.
• PMID:18163131 (The emerging landscape of breast cancer susceptibility): 'In CHEK2, ATM, BRIP1 and PALB2, most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay through nonsense codons or translational frameshifts. A small proportion is likely to be rare missense variants that disrupt critical functions.' This establishes that missense is a minority, not a common, disease mechanism in CHEK2.
• No gene-level benign-missense constraint metric was provided in the case evidence; the only missense data supplied are the three functional-assay papers and the single-variant gnomAD frequency, which do not measure the gene's rate of benign missense variation.

Still missing

• No gene-level benign-missense-constraint metric (missense Z-score or benign-missense rate for CHEK2) was available in this case, so the first PP2 precondition could not be positively established.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable PP2 rule, so the generic ACMG/AMP 2015 definition was used.

Sources

Reasoning

NM_007194.4:c.1561C>T encodes the missense substitution NP_009125.1:p.(Arg521Trp) in CHEK2 exon 15 (no intronic/splice-region involvement), so the applicable PP3/BP4 path is the missense protein-impact path, REVEL, and not SpliceAI. The local REVEL score for this variant is 0.205, which is below the ClinGen SVI supporting PP3 threshold of >=0.644 (and therefore far below the moderate 0.773 and strong 0.932 cutoffs). PP3 is not met. The SpliceAI result (max delta 0.006) is out of scope for a missense variant and was not used as PP3 support. BayesDel (score -0.0743) was disregarded because no generic ACMG-strength BayesDel calibration is established and the governing CHEK2 specification provides no cutoff. The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification for CHEK2 v1.0 (CSPEC doc 522546466) carries no structured gene-specific PP3/BP4 computational rule, so the generic ClinGen SVI REVEL calibration applies.

Rule

Missense variant: PP3 requires REVEL >= 0.644 (supporting), >= 0.773 (moderate), or >= 0.932 (strong), per ClinGen SVI REVEL calibration (PMID:36413997).

Evidence considered

• Variant NM_007194.4:c.1561C>T encodes a missense substitution NP_009125.1:p.(Arg521Trp) in CHEK2 exon 15; the consequence type selects the REVEL protein-impact path for PP3/BP4, not the SpliceAI splice path.
• Local REVEL score for this variant is 0.205 (source: local REVEL v1.3 lookup, chrom 22 GRCh38 position 28687968 G>A).
• REVEL 0.205 is below the ClinGen SVI supporting PP3 threshold of >=0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997), so no PP3 weight (supporting, moderate, or strong) is reached.
• BayesDel score -0.0743 was disregarded: no generic ACMG-strength BayesDel calibration exists and the CHEK2 VCEP specifies no cutpoint.
• SpliceAI max delta score 0.006 was not used for PP3; it is out of scope for a missense variant and is not evidence for the protein-impact prediction.
• The governing framework is the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification for CHEK2 v1.0 (CSPEC doc 522546466); its rule payload contains no gene-specific PP3/BP4 computational thresholds, so the generic ClinGen SVI REVEL calibration is applied.

Sources

Reasoning

PP4 requires that the patient's phenotype or family history be highly specific for a disease with a single genetic etiology. The phenotype associated with CHEK2 is a genetically heterogeneous, moderate-penetrance cancer predisposition (hereditary breast/ovarian cancer, with broader cancer risk) that is caused by many genes (e.g., BRCA1, BRCA2, PALB2, ATM) and is common in the population; it is therefore not highly specific to CHEK2. PMID:18163131 places CHEK2 within exactly this group of rare moderate-penetrance breast cancer susceptibility genes with a roughly two- to fourfold relative risk, which is by definition a non-specific, shared phenotype. In addition, the case record contains no proband-level phenotype or family history on which specificity could be judged. PP4 is not met.

Rule

ACMG/AMP 2015 PP4 (supporting): patient's phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• ACMG/AMP 2015 (PMID:25741868) defines PP4 as a patient's phenotype or family history that is highly specific for a disease with a single genetic etiology.
• PMID:18163131 reviews CHEK2 as a rare moderate-penetrance breast cancer susceptibility gene (approximately two- to fourfold relative risk) belonging to a genetically heterogeneous group (CHEK2, ATM, BRIP1, PALB2); the associated cancer phenotype is shared across multiple genes and is therefore not specific to CHEK2.
• No proband phenotype or family history was available in the case bundle, so specificity could not be established for this individual.

Still missing

• No proband-level phenotype or family history is present in the case record, so PP4 specificity cannot be evaluated against this individual's presentation.

Sources

Reasoning

PP5 (supporting) may be applied only when there is an exact-variant classification from a recognized expert panel / reputable source reporting the variant as Pathogenic or Likely pathogenic. The ClinVar record for this variant (ClinVarID 140881, VCV000140881) is Uncertain significance and contains zero expert-panel submissions (expert_panels is empty; expert_panel_submissions = 0). All submissions are ordinary laboratory submissions (or no-criteria submissions) and the aggregate review status is 'criteria provided, multiple submitters, no conflicts' (2 stars); there is no pathogenic assertion from any source. Under the governing rule for this group, ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger PP5. Because no qualifying exact-variant expert-panel pathogenic classification exists, PP5 is not met.

Rule

PP5 (supporting): reputable source / expert panel reports the exact variant as Pathogenic or Likely pathogenic; only an exact-variant ClinVar expert-panel classification qualifies for this group.

Evidence considered

• ClinVar VCV000140881 (ClinVarID 140881): classification Uncertain significance; review status 'criteria provided, multiple submitters, no conflicts' (2 stars); expert_panels {} and expert_panel_submissions = 0; 15-16 laboratory submissions, none from a recognized expert panel.
• ACMG/AMP 2015 (PMID:25741868) PP5 requires a reputable source reporting the variant as pathogenic; per the governing rule for this group only an exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classification qualifies, and no such classification exists.

Sources

Reasoning

BA1 (stand-alone benign) requires an allele frequency at or above 0.05 (ACMG/AMP 2015; PMID:25741868). CHEK2 c.1561C>T (p.Arg521Trp) is far below this in every source. gnomAD v4.1: overall AF 4.51131e-05 (72/1,595,990 alleles; 0 homozygotes), highest ancestry group East Asian AF 0.0005794 (26/44,874), grpmax (popmax) FAF 0.0004053. gnomAD v2.1: overall AF 5.29069e-05 (14/264,616; 0 homozygotes), East Asian AF 0.000409165 (8/19,552), grpmax FAF 0.00022085. Even the most extreme subpopulation value collected anywhere (1KG:JPT, gnomAD v3.1 non-cancer genomes, 1/204 = 0.0049) sits more than ten-fold below 0.05. No dataset approaches the BA1 threshold, so BA1 is not met.

Rule

BA1 met if population allele/FAF >= 0.05 (ACMG/AMP 2015 stand-alone benign; PMID:25741868)

Evidence considered

• gnomAD v4.1 total AF 4.51131e-05 (72/1,595,990 alleles, 0 homozygotes); grpmax (popmax) FAF 0.0004053; highest ancestry group East Asian AF 0.0005794 (26/44,874 alleles, 0 homozygotes).
• gnomAD v2.1 total AF 5.29069e-05 (14/264,616 alleles, 0 homozygotes); grpmax FAF 0.00022085; highest ancestry group East Asian AF 0.000409165 (8/19,552 alleles, 0 homozygotes).
• Applied the generic ACMG/AMP 2015 BA1 stand-alone benign threshold of >=0.05 (PMID:25741868). No CHEK2-VCEP-specific population-frequency threshold was extractable from the governing specification for this case, so the generic default was used.
• Every observed frequency, including the highest subpopulation value (1KG:JPT 1/204 = 0.0049 in gnomAD v3.1 non-cancer genomes), is well under 0.05.

Sources

Reasoning

BS1 (strong benign) requires an allele frequency at or above the gene-specific expected maximum, for which the generic SVI default used here is 0.01 (Whiffin et al. 2017; PMID:28518168, as adopted in the supplied calibration). CHEK2 c.1561C>T (p.Arg521Trp) does not reach this. The highest observed values are the gnomAD v4.1 grpmax (popmax) FAF of 0.0004053 (East Asian, 26/44,874 alleles) and the gnomAD v2.1 grpmax FAF of 0.00022085 (East Asian, 8/19,552 alleles); overall AFs are 4.51131e-05 (v4.1, 72/1,595,990) and 5.29069e-05 (v2.1, 14/264,616), with 0 homozygotes in both. The maximum value is roughly 25-fold below the 0.01 threshold, so BS1 is not met.

Rule

BS1 met if population allele/FAF >= 0.01 (generic SVI default, per-gene derivation preferred; PMID:28518168)

Evidence considered

• gnomAD v4.1 total AF 4.51131e-05 (72/1,595,990 alleles, 0 homozygotes); grpmax (popmax) FAF 0.0004053; East Asian AF 0.0005794 (26/44,874).
• gnomAD v2.1 total AF 5.29069e-05 (14/264,616 alleles, 0 homozygotes); grpmax FAF 0.00022085; East Asian AF 0.000409165 (8/19,552).
• Applied the generic SVI strong-benign threshold of >=0.01, whose per-gene derivation is from Whiffin et al. 2017 (PMID:28518168); that publication is not itself a source_registry key for this case, so it is named here rather than in evidence_refs. No CHEK2-VCEP-specific BS1 threshold was extractable for this case, so the generic default was used.
• The highest frequency seen anywhere in the collected population data (1KG:JPT 1/204 = 0.0049) remains below 0.01.

Sources

Reasoning

BS3 requires well-established functional studies demonstrating no damaging effect on the gene or gene product (Richards et al. 2015, PMID:25741868). One assay supports BS3: PMID:30851065 categorized p.(Arg521Trp) as benign in an in vivo yeast MMS-growth assay, with growth comparable to the WT positive control and distinct from the non-functional c.1100delC negative control. However, that benign readout is directly contradicted by two other functional datasets. In PMID:34903604, p.R521W was among nine missense variants showing an intermediate defect in CHK2-mediated KAP1 p.S473 phosphorylation in a mouse-ES complementation assay, i.e. demonstrably not wild-type. In PMID:37449874, p.R521W was classified as functionally impaired on the basis of severely aberrant nuclear localization in the ScanR readout, again inconsistent with a clean no-damaging-effect conclusion. Because at least two independent, controlled assays show a functional abnormality for this variant, the ACMG requirement that functional studies establish no damaging effect is not satisfied, so BS3 is not met at any strength. The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) is present but supplied no extractable BS3 functional-assay specification (framework_complete=false, empty rule payload), so the generic ACMG/AMP 2015 BS3 definition was applied and no VCEP-calibrated functional strength was available.

Rule

BS3 requires well-established functional studies showing no damaging effect; a single benign yeast result contradicted by intermediate and impaired-localization assays does not meet the criterion (Richards et al. 2015).

Evidence considered

• BS3 (Richards et al. 2015, PMID:25741868) is met when well-established functional studies show no damaging effect on the gene or gene product; the gene-agnostic ACMG/AMP 2015 definition was applied because the CHEK2 CSPEC provided no functional-assay ruleset.
• PMID:30851065 (in vivo yeast S. cerevisiae MMS-growth assay, RAD53/SML1-deleted strain; WT positive control and c.1100delC negative control; 120 CHEK2 missense variants): p.(Arg521Trp) was categorized benign, with growth comparable to wild type; direct quote: "On the contrary, variants p.(Tyr159His), p.(Asp203Gly), p.(Tyr327Cys), p.(Ala334Thr), p.(Gly342Ser), p.(Glu377Gly), and p.(Arg521Trp), which were categorized as benign by the yeast functional assay, were predicted as damaging and/or possibly damaging by in silico predictions (detailed results are shown in Table 1)." This single assay would support BS3, but benign categorization required normalized median >0.70 and normalized standardized difference of means >0.30, and the result was discordant with in silico prediction.
• PMID:34903604 (mouse embryonic stem-cell complementation assay; CHK2-mediated KAP1 p.S473 phosphorylation after IR, FACS readout): p.R521W was among nine variants with an INTERMEDIATE functional defect, i.e. demonstrably not wild-type, which argues against a no-damaging-effect conclusion.
• PMID:37449874 (ENIGMA CHEK2gether; KAP1/CHK2 kinase assays plus ScanR nuclear-localization readout): p.R521W was included among the 102 functionally impaired variants because it was one of only two analyzed missense variants with severely impaired nuclear localization, inconsistent with a purely benign functional readout.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466; case framework source cspec_ruleset, framework_complete=false, empty rule_payload) contained no extractable BS3 functional-assay specification or calibrated strength.

Still missing

• BS3 cannot be met while the mouse-ES intermediate KAP1-phosphorylation defect (PMID:34903604) and the ENIGMA impaired-localization classification (PMID:37449874) remain uncontradicted; the discordance across assays prevents a confident no-damaging-effect conclusion.
• The yeast assay (PMID:30851065) is a single in vivo model; no independent replication of its benign result for p.Arg521Trp was identified in the fetched literature.
• The governing CHEK2 CSPEC (ClinGen HBOP CHEK2 v1.0, doc 522546466) supplied no extractable BS3 functional-assay rules or calibrated strength, so no VCEP-specific BS3 calibration could be applied.

Sources

Reasoning

BP2 (benign, supporting) requires observation of the variant either in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant under any inheritance model. No second CHEK2 variant, no phase-resolved genotype, and no family segregation data were identified for NM_007194.4:c.1561C>T in any source; the variant is reported only as a single heterozygous change of uncertain significance (ClinVar 140881) with no trans or cis assertion. The specific allelic configuration BP2 depends on is therefore absent, so the criterion is not met. Independently, CHEK2 is a moderate-penetrance breast cancer predisposition gene rather than the 'fully penetrant' dominant gene the trans arm of BP2 presumes, which further distances this variant from the criterion's premise.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern (Richards et al. 2015, PMID:25741868).

Evidence considered

• ACMG/AMP 2015 standards (PMID:25741868) define BP2 as observation of the variant in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or in cis with a pathogenic variant in any inheritance pattern.
• The governing CHEK2 HBOP specification (cspec) assigns an autosomal dominant mode of inheritance (MONDO:0700271) but provides no variant-level BP2 modification for this variant.
• No phase, family, or co-occurring-variant data were identified for c.1561C>T in the case evidence; ClinVar (140881) lists it as a single heterozygous variant of uncertain significance with no trans/cis assertion.
• CHEK2 is a moderate-penetrance breast cancer predisposition gene (PMID:18163131, approximately two- to fourfold relative risk), not the 'fully penetrant' dominant gene assumed by the trans arm of BP2.
• The ENIGMA CHEK2gether study (PMID:37449874) functionally categorized p.R521W but reports no per-variant phase or family data, so it contributes nothing to the allelic configuration BP2 requires.
• With no pathogenic allele present in trans (or in cis), the specific observation BP2 requires is absent; BP2 is not met.

Still missing

• No phase-resolved (trans/cis) genotype, co-occurring pathogenic CHEK2 allele, or family segregation data exist for NM_007194.4:c.1561C>T; BP2 cannot be supported without such an observation.

Sources

Reasoning

BP6 (supporting) may be applied only when there is an exact-variant classification from a recognized expert panel / reputable source reporting the variant as Benign or Likely benign. The ClinVar record for this variant (ClinVarID 140881, VCV000140881) is Uncertain significance, with zero expert-panel submissions and no benign assertion from any source; the aggregate review status is 2-star ('criteria provided, multiple submitters, no conflicts'). Under the governing rule for this group, ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger BP6. Because no qualifying exact-variant expert-panel benign classification exists, BP6 is not met.

Rule

BP6 (supporting): reputable source / expert panel reports the exact variant as Benign or Likely benign; only an exact-variant ClinVar expert-panel classification qualifies for this group.

Evidence considered

• ClinVar VCV000140881 (ClinVarID 140881): classification Uncertain significance; 2-star review status; expert_panels {} and no expert-panel submissions; no Benign or Likely benign assertion present from any submitter.
• ACMG/AMP 2015 (PMID:25741868) BP6 requires a reputable source reporting the variant as benign; per the governing rule for this group only an exact-variant ClinVar expert-panel Benign/Likely benign classification qualifies, and no such classification exists.

Sources

Reasoning

PS2 requires a de novo occurrence of the variant in a proband affected with the CHEK2-related phenotype, with both maternity and paternity confirmed by parental testing. This case provides no proband, no parental genotypes, and no family history: it is a variant-level assessment of NM_007194.4:c.1561C>T (NP_009125.1:p.(Arg521Trp)) with no individual carrying the variant reported anywhere. The ClinVar record (variation 140881) aggregates submissions from 15-16 laboratories, all classifying the variant as Uncertain significance (criteria provided, multiple submitters, no conflicts, no expert-panel submission), and none of the attached submissions or their cited PMIDs reports a de novo occurrence or trio data for this variant. The governing CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification (CSPEC doc 522546466) is present but exposes no criterion-level PS2 rule (unstructured ruleset, empty rule payload), so the generic ACMG/AMP 2015 PS2 definition applies. De novo status therefore cannot be established or excluded, and PS2 is left not assessed for want of proband and parental data.

Evidence considered

• PS2 (Richards et al. 2015, ACMG/AMP, PMID:25741868) requires a de novo variant in a patient affected with the relevant phenotype, with maternity and paternity confirmed by parental testing.
• The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification v1.0 (CSPEC doc 522546466) governs this gene but was captured as an unstructured ruleset with an empty rule payload, so no gene-specific PS2 modification applies and the generic ACMG/AMP 2015 definition is used.
• The ClinVar record for variation 140881 (CHEK2 c.1561C>T) lists roughly 15-16 submitters, all Uncertain significance with no conflicts and no expert-panel submission, and none of the submissions or their cited PMIDs reports a de novo event or trio testing for this variant.
• No proband, parental genotypes, family history, or phenotype-consistency information is present for this variant; the assessment is variant-level only.

Still missing

• No affected proband is provided, so a de novo occurrence of c.1561C>T cannot be observed.
• No parental (trio or parent-only) genotype testing is available to confirm maternity and paternity.
• No phenotype-consistency or family-history information accompanies this variant-level case.

Sources

Reasoning

PM6 covers an assumed de novo occurrence without confirmation of maternity and paternity; it still requires at least one affected proband in whom the variant was observed and attributed to a de novo event. This case reports no proband and no individual carrying NM_007194.4:c.1561C>T, and there is no parental or pedigree information from which even an unconfirmed de novo event could be inferred. The ClinVar record (variation 140881) is confined to classification summaries (all Uncertain significance) and reports no de novo observation for this variant. The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification (CSPEC doc 522546466) supplies no criterion-level PM6 rule (unstructured ruleset, empty rule payload), so generic ACMG/AMP 2015 applies. With no proband-level observation, PM6 cannot be assessed.

Evidence considered

• PM6 (Richards et al. 2015, ACMG/AMP, PMID:25741868) applies to an assumed de novo occurrence observed in an affected proband but without confirmation of maternity and paternity.
• No proband and no carrier of NM_007194.4:c.1561C>T is described in this case; the assessment is variant-level only.
• The ClinVar record for variation 140881 (CHEK2 c.1561C>T) contains only classification summaries (all Uncertain significance) and no de novo observation for this variant.
• The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification v1.0 (CSPEC doc 522546466) was captured as an unstructured ruleset with an empty rule payload and provides no PM6-specific rule, so the generic ACMG/AMP 2015 definition governs.

Still missing

• No proband carrying c.1561C>T is reported, so no assumed de novo observation exists.
• No parental testing or pedigree is available to characterise the event, even without maternity/paternity confirmation.

Sources

Reasoning

PP1 requires co-segregation of the variant with disease across multiple affected members of a family. This case contains no pedigree and no genotype-phenotype data from relatives for NM_007194.4:c.1561C>T. The single source triaged under the segregation theme, Xu et al. 2020 (PMID:32973888), is a comparison of Lynch-like versus Lynch syndrome in a colorectal cancer cohort analysed for mismatch-repair and selected non-MMR genes; its full text neither names CHEK2 nor the c.1561C>T/p.(Arg521Trp) change, so it contributes no co-segregation evidence. The ClinVar record for variation 140881 likewise provides no family segregation data, and no other source in this case reports meioses or pedigrees. The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification (CSPEC doc 522546466) exposes no criterion-level PP1 rule (unstructured ruleset), so generic ACMG/AMP 2015 applies. With no family data, co-segregation cannot be evaluated.

Evidence considered

• PP1 (Richards et al. 2015, ACMG/AMP, PMID:25741868) requires co-segregation of the variant with the disease in multiple affected family members of a gene definitively known to cause the disease.
• The only source triaged under the segregation theme, Xu et al. 2020 (PMID:32973888), is a Lynch-like versus Lynch syndrome colorectal cancer pedigree comparison analysing mismatch-repair and selected non-MMR genes; it does not mention CHEK2, c.1561C>T, or p.(Arg521Trp) and yields no co-segregation evidence.
• The ClinVar record for variation 140881 (CHEK2 c.1561C>T) reports only classification summaries (all Uncertain significance) and no family segregation analyses.
• The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification v1.0 (CSPEC doc 522546466) was captured as an unstructured ruleset with an empty rule payload and provides no PP1-specific rule, so the generic ACMG/AMP 2015 definition governs.

Still missing

• No pedigree or genotype data from affected relatives is available, so co-segregation cannot be tested.
• No meiosis count, segregation ratio, or family linkage information is present for this variant.
• The only segregation-themed source (PMID:32973888) does not mention CHEK2 or c.1561C>T and provides no family data.

Sources

Reasoning

BS4 requires demonstration that the variant does not segregate with disease in affected members of a family, evidence that would argue against pathogenicity. This case provides no pedigree and no genotype data from affected or unaffected relatives for NM_007194.4:c.1561C>T, so non-segregation cannot be shown. The segregation-themed source (PMID:32973888, Xu et al. 2020) does not report CHEK2 or this variant and therefore contains no non-segregation data; the ClinVar record (variation 140881) likewise reports no family analyses, and no other source supplies relative genotypes. The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification (CSPEC doc 522546466) has no extracted criterion-level BS4 rule (unstructured ruleset, empty rule payload), so generic ACMG/AMP 2015 applies. BS4 is left not assessed for lack of family data.

Evidence considered

• BS4 (Richards et al. 2015, ACMG/AMP, PMID:25741868) requires lack of segregation of the variant with disease in affected members of a family as evidence against pathogenicity.
• No pedigree or relative genotypes are present for NM_007194.4:c.1561C>T, so non-segregation cannot be evaluated for this variant.
• Xu et al. 2020 (PMID:32973888), the only segregation-themed source, analyses mismatch-repair genes in a colorectal cancer cohort and does not mention CHEK2 or c.1561C>T; it contains no non-segregation data.
• The CHEK2 Hereditary Breast, Ovarian and Pancreatic Cancer VCEP specification v1.0 (CSPEC doc 522546466) was captured as an unstructured ruleset with an empty rule payload and provides no BS4-specific rule, so the generic ACMG/AMP 2015 definition governs.

Still missing

• No pedigree or relative genotype data is available, so lack of segregation cannot be demonstrated.
• The only segregation-themed source (PMID:32973888) does not mention CHEK2 or c.1561C>T and provides no non-segregation data.

Sources

Reasoning

BP5 requires documentation that this variant was found in a case in which an alternate molecular basis for the disease was established (e.g., a co-occurring pathogenic variant in another gene, or a distinct molecular diagnosis). The case record contains no proband- or case-level data of any kind: no co-occurring pathogenic variant, no second molecular diagnosis, and no family data are provided. Without any case context, the presence or absence of an alternate molecular basis cannot be determined. The criterion is not supported by available evidence, but because the underlying evidence is simply absent rather than negative, it is returned as not_assessed to identify the gap.

Rule

ACMG/AMP 2015 BP5 (supporting): variant detected in a patient with an alternate molecular basis for disease.

Evidence considered

• ACMG/AMP 2015 (PMID:25741868) defines BP5 as a variant detected in a patient with an alternate molecular basis for disease (e.g., a different causal variant or diagnosis); no case-level information of this kind is present in the record.

Still missing

• No case-level/proband data (co-occurring pathogenic variant in another gene, or an established alternate molecular diagnosis) are available in the record to evaluate BP5.

Sources