CHEK2 c.1100del, p.Thr367MetfsTer15

Reasoning

NM_007194.4:c.1100del is a one-nucleotide deletion causing the frameshift NP_009125.1:p.(Thr367MetfsTer15), truncating the 544-residue CHEK2 protein after residue 366 and predicting termination at residue 381. The variant is in exon 11 of the 14-exon coding transcript, well before the terminal exon, so the premature termination is expected to undergo nonsense-mediated decay rather than escape it; the affected transcript is the validated MANE/RefSeq transcript used for the case. CHEK2 loss of function is a recognized germline disease mechanism, and the exact CHEK2*1100delC allele is reported as a truncating variant that abrogates kinase activity. No named downgrade rule is supported: this is not an NMD-escaping truncation, a terminal/non-critical distal truncation, or a variant in a gene without an established LOF mechanism. Therefore PVS1 is met at full strength, recorded as the literal tier "very strong".

Rule

PVS1: Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease. ... Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7).

Evidence considered

• Variant-level assessment identifies NM_007194.4:c.1100del as a frameshift in exon 11, producing NP_009125.1:p.(Thr367MetfsTer15) and suggesting default PVS1 strength of very strong under the generic ClinGen SVI framework.
• Transcript normalization gives NP_009125.1:p.(Thr367MetfsTer15); the predicted protein terminates at residue 381 versus the original residue 544, with the variant located in exon 11 of 14 coding exons.
• Meijers-Heijboer et al. explicitly describe CHEK2*1100delC as "a truncating variant that abrogates the kinase activity" and report disease-associated segregation and case-control enrichment for the exact allele.

Sources

Reasoning

PS3 is met at supporting strength. The exact CHEK2*1100delC allele, corresponding to NM_007194.4:c.1100del and p.(T367Mfs*15), was reported to abrogate CHEK2 kinase activity. This is direct variant-specific functional evidence in a biologically relevant kinase assay context, supporting loss of protein function. The available evidence does not establish the reproducibility, robustness, or clinical-diagnostic-laboratory validation required for a stronger functional designation, and no independent variant-specific functional replication or detailed assay-control data are documented here.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Meijers-Heijboer et al. 2002, abstract and functional statement: CHEK2*1100delC, corresponding to the case variant c.1100del/p.(T367Mfs*15), is described as a truncating variant that abrogates CHEK2 kinase activity.
• The same study provides variant-specific breast-cancer family and case-control observations, but those observations were not used to establish PS3; the PS3 evidence is the reported kinase-activity effect.
• A separate study of non-identical C-terminal Chk2 frameshift mutants reported loss of kinase activity in vitro, but it was not used as primary variant-specific evidence because c.1100del was not explicitly tested.

Still missing

• Independent replication of the exact variant-specific assay result is not documented.
• Detailed assay controls and validation in a clinical diagnostic laboratory setting are not documented.

Sources

Reasoning

PS4 is met under the generic ACMG/AMP rule. PMID:11967536 explicitly reports CHEK2*1100delC, corresponding to this exact c.1100del frameshift, in affected individuals and healthy controls. In the breast-cancer families containing male breast cancer, the allele occurred in 7/52 affected individuals versus 18/1620 healthy controls. Treating this as a case-control comparison, I calculated OR = (7 x 1602)/(45 x 18) = 13.84 with an approximate Wald 95% CI of 5.51-34.81; the inequality is 13.84 > 5.0? yes, and the CI excludes 1.0. The broader affected-family comparison was 55/1071 versus 18/1620, OR 4.82 (95% CI 2.81-8.25), which does not independently exceed 5. PMID:28779002 independently reports the exact c.1100delC variant in 13,087 cases and 5,488 controls with OR 3.18 (95% CI 2.01-4.92), supporting enrichment but not independently meeting the >5 threshold. The male-breast-cancer-family comparison in PMID:11967536 supplies the qualifying PS4 evidence.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• PMID:11967536, Abstract and Results/Table 1: CHEK2*1100delC was present in 7/52 affected individuals from BRCA1/BRCA2-negative families containing male breast cancer and 18/1620 healthy controls; the exact variant was also present in 55/1071 affected individuals from the broader affected-family cohort.
• PMID:11967536, computed case-control comparison from the reported counts: OR=(7/45)/(18/1602)=13.84; approximate Wald 95% CI=5.51-34.81. Explicit threshold check: 13.84 > 5.0? yes; CI excludes 1.0.
• PMID:28779002, Results, BC risks associated with ATM, CHEK2 and PALB2 truncating variants: exact CHEK2 c.1100delC (p.Thr367MetfsTer15) was associated with OR=3.18 (95% CI 2.01-4.92) in 13,087 breast-cancer cases and 5,488 controls.
• The literature_pass ai-classified PS4 leads were checked against the available abstract/full-text extracts: PMID:11967536 confirms exact-variant affected/control frequencies; PMID:18172190 reports a meta-analysis of 26,000 cases and 27,000 controls; PMID:21876083 reports affected patients and controls; PMID:21956126 reports Danish/German case-control studies; PMID:25431674 and PMID:26629066 report prostate-cancer associations. The qualifying numeric comparison used here is the exact-variant case/control count comparison from PMID:11967536, with independent support from PMID:28779002.

Sources

Reasoning

The variant-specific family study assessed 20 BRCA1/BRCA2-negative families in which an index case carried CHEK2*1100delC and at least one other affected individual was typed. Among 27 additional affected individuals, 16 (59%) carried the variant, compared with 41% expected if unrelated to breast cancer; the estimated relative risk was 2.2 (P=0.049). This is co-segregation with disease in multiple affected family members and supports PP1 at supporting strength; no supplied rule threshold justifies a stronger level.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.

Evidence considered

• Li et al. 2002, PMID:11967536, Results: 20 BRCA1/BRCA2-negative families were assessed; 27 additional affected individuals were typed, and 16 (59%) carried CHEK2*1100delC versus 41% expected if the variant were unrelated to breast cancer (estimated relative risk 2.2, P=0.049).
• The study used family segregation analysis and statistical analysis with MENDEL; the observed co-segregation supports PP1, but the prompt supplies no quantitative threshold for upgrading PP1 beyond supporting strength.

Sources

Reasoning

PM2 is not met because the variant is present in population controls at frequencies well above the generic supporting threshold of 0.0001. The governing non-cancer exome source reports AF=0.0020515751490697534 (481/234,454 alleles; zero homozygotes) in gnomAD v2.1, and the non-cancer genome-only source reports AF=0.001709990943130973 (253/147,954 alleles; zero homozygotes) in gnomAD v3.1. gnomAD v4.1 all-comers independently reports AF=0.0021516173435128147. These frequencies are approximately 0.17%-0.22%, not absent or extremely low.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• GNOMAD_V2_1_NON_CANCER exomes specifically: 481/234,454 alleles, AF=0.0020515751490697534, homozygotes=0.
• GNOMAD_V3_1_NON_CANCER genomes only because v3 has no exome cohort: 253/147,954 alleles, AF=0.001709990943130973, homozygotes=0.
• gnomAD v4.1 all-comers: 3,467/1,611,346 alleles, AF=0.0021516173435128147, homozygotes=5.
• The supplied generic calibration threshold for PM2 Supporting is <= 0.0001, identified as the ClinGen SVI 2020 recommendation (PMID:25741868).

Sources

Reasoning

PP5 is not met. ClinVar reports the exact variant as Pathogenic, but the case evidence records zero expert-panel submissions; the available assertions are ordinary laboratory, aggregate, or non-expert assertions. Under the specified generic rule, those sources cannot trigger PP5.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar exact-variant record NM_007194.4(CHEK2):c.1100del (p.Thr367fs), Variation ID 128042, is summarized as Pathogenic, but the submission audit reports expert_panel_submissions=0 and identifies the available assertions as non-expert submissions; therefore the generic PP5 requirement is not satisfied.

Sources

Reasoning

BA1 is not met. The highest observed frequency is 0.008722319579416918 (0.872%) in gnomAD v2.1 non-cancer Finnish exomes, below the generic stand-alone threshold of 0.05 (5%). The overall non-cancer exome frequency is 0.0020515751490697534, and gnomAD v4.1 all-comers frequency is 0.0021516173435128147; neither approaches 5%. The variant is an indel, so the governing caveat about potentially poor next-generation sequencing calls is relevant, but the large allele counts and concordant observations provide usable population data.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• GNOMAD_V2_1_NON_CANCER exomes: 481/234,454 alleles, AF=0.0020515751490697534, homozygotes=0; Finnish AF=0.008722319579416918 (219/25,108).
• gnomAD v4.1 all-comers: 3,467/1,611,346 alleles, AF=0.0021516173435128147, homozygotes=5; Finnish AF=0.008572499297336124 (549/64,042).
• The variant is an indel (22-28695868-AG-A; rs555607708); the governing ACMG/AMP text cautions that indel population data may be poorly called by next-generation sequencing, but the available allele counts are substantial and the frequency observations are concordant.

Sources

Reasoning

BP6 is not met. The exact-variant ClinVar record is Pathogenic rather than Benign or Likely benign, and the submission audit reports zero expert-panel submissions. No qualifying reputable expert-panel benign assertion is available.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar exact-variant record NM_007194.4(CHEK2):c.1100del (p.Thr367fs), Variation ID 128042, is summarized as Pathogenic with zero expert-panel submissions; no qualifying expert-panel Benign or Likely benign assertion is present.

Sources

Reasoning

No case-specific report documents this variant as de novo in a proband with confirmed maternity and paternity, and no evidence establishes absence of a family history. The available variant-specific family study concerns inherited CHEK2*1100delC in families with affected relatives rather than a de novo occurrence.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• PMID:11967536 studied CHEK2*1100delC in 20 families in which an index case carried the variant and at least one other individual with breast cancer was typed; this is familial segregation evidence, not a de novo report.
• No case evidence documents confirmed maternity and paternity for a proband with CHEK2 c.1100del or establishes no family history.

Still missing

• Proband-level de novo documentation is unavailable.
• Both maternity and paternity confirmation are unavailable.
• A documented negative family history for the relevant disease is unavailable.

Sources

Reasoning

No case-specific report documents an assumed de novo occurrence of CHEK2 c.1100del without parental confirmation. The available variant-specific publication reports familial segregation and does not provide a de novo proband observation.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• PMID:11967536 reports inherited familial CHEK2*1100delC segregation, not an assumed de novo case.
• No source reviewed documents a de novo event with unconfirmed maternity and/or paternity for this variant.

Still missing

• A proband-level de novo observation is unavailable.
• The parental testing status for any proband is unavailable.

Sources

Reasoning

The governing PP4 rule requires a patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The available case evidence does not provide an individual patient's phenotype or a sufficiently specific family history for this assessment; population case-control cancer associations cannot substitute for the patient's phenotype.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Still missing

• Patient phenotype and detailed family history are not available in the supplied evidence.

Reasoning

BS1 is not assessed from the generic 1% default. The observed frequency is 0.0020515751490697534 in gnomAD v2.1 non-cancer exomes and 0.0021516173435128147 in gnomAD v4.1 all-comers, while the Finnish founder-enriched frequency is 0.008722319579416918, below 1%. CHEK2 c.1100delC is a known reduced-penetrance, founder-enriched breast-cancer susceptibility allele; Meijers-Heijboer et al. reported it in 18/1,620 healthy controls (1.1%). Because BS1 asks whether the frequency is greater than expected for the disorder, a maximum-credible-allele-frequency calculation using explicit prevalence, penetrance, and allelic-heterogeneity inputs is required before applying it, and no case-specific calculation is available.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• GNOMAD_V2_1_NON_CANCER exomes: AF=0.0020515751490697534 (481/234,454); Finnish AF=0.008722319579416918 (219/25,108).
• gnomAD v4.1 all-comers: AF=0.0021516173435128147 (3,467/1,611,346); Finnish AF=0.008572499297336124 (549/64,042).
• Meijers-Heijboer et al. 2002 (PMID:11967536): CHEK2*1100delC was observed in 18/1,620 healthy controls (1.1%) and characterized as a low-penetrance breast-cancer susceptibility allele with a common founder background.
• Whiffin et al. 2017 (PMID:28518168) is the named publication for maximum-credible-allele-frequency assessment; the required case-specific prevalence, penetrance, and allelic-heterogeneity inputs and calculation are not available.

Still missing

• A disorder-specific maximum credible allele frequency calculation with explicit prevalence, penetrance, and allelic-heterogeneity inputs is unavailable.

Sources

Reasoning

BS3 is not assessed because the available evidence does not show that CHEK2 c.1100del has no damaging effect on protein function or splicing. The reported variant-specific functional evidence instead describes loss of kinase activity, which addresses PS3 rather than BS3.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Still missing

• A well-established variant-specific assay demonstrating preserved CHEK2 protein function or normal splicing is not available.

Reasoning

The available family study does not document affected relatives who lack CHEK2*1100delC; instead, 16 of 27 additional affected individuals carried the variant. No independent family-level non-segregation observation is available, and absence of such a report cannot establish lack of segregation.

Rule

Lack of segregation in affected members of a family. ... Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals.

Evidence considered

• PMID:11967536 reports 16 of 27 additional affected individuals carrying CHEK2*1100delC and describes only limited/partial segregation; it does not provide a qualifying affected-noncarrier family observation for BS4.
• The BS4 caveat is relevant because breast cancer is a common phenotype, but the available source does not provide the family-level information needed to resolve phenocopies or an alternative pathogenic variant.

Still missing

• No affected noncarrier relatives are documented for a family suitable for BS4 assessment.
• No family-level analysis addressing phenocopies or other pathogenic variants is available.

Sources

Reasoning

BP2 requires either observation in trans with a pathogenic variant for a fully penetrant dominant disorder or observation in cis with a pathogenic variant. CHEK2-related cancer predisposition is identified as autosomal dominant, but the available evidence does not establish that it is a fully penetrant dominant disorder and does not document a pathogenic second allele, cis phase, or trans phase for this variant. The available family study reports affected carriers and segregation of CHEK2*1100delC but does not provide the phase relationship required for BP2.

Rule

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.

Evidence considered

• ClinGen CHEK2 framework, raw rule origin: preferred mode of inheritance is "Autosomal dominant inheritance" for CHEK2-related cancer predisposition.
• Meijers-Heijboer et al. 2002, family segregation results: CHEK2*1100delC was found in 16 of 27 additional affected individuals in 20 variant-positive families; the reported study does not document a pathogenic second allele or cis/trans phase for this variant.

Still missing

• Parental or offspring testing and an identified pathogenic second allele are needed to establish cis or trans phase.
• Evidence establishing full penetrance of the CHEK2-related disorder would be needed for the BP2 trans path.

Sources

Reasoning

No evidence in the supplied case materials establishes that this variant was found in a case with an alternate molecular basis for disease. Cancer case-control associations and ClinVar classifications do not establish an alternate molecular diagnosis for an individual case.

Rule

Variant found in a case with an alternate molecular basis for disease.

Still missing

• No documented individual case with a confirmed alternate molecular diagnosis is available.