CHEK2 c.1247T>C, p.Ile416Thr

Reasoning

PM2 is met at supporting strength under the supplied generic SVI threshold. The default all-comers gnomAD v4.1 data show one observed allele among 1613712 total alleles (AF=6.196892630159533e-07), zero homozygotes, and the variant was absent from gnomAD v2.1. The observed frequency is below the supplied PM2 supporting threshold of 0.0001. No VCEP-specific PM2 source or threshold is released for CHEK2, so the all-comers gnomAD v4.1 entry is the governing default.

Rule

PM2: 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: absent.
• gnomAD v4.1 all-comers: AF=6.196892630159533e-07, 1/1613712 alleles, homozygotes=0; the only observed allele was in European non-Finnish individuals (AF=8.477176896641173e-07, 1/1179638 alleles, homozygotes=0).
• The CHEK2 specification is listed on CSPEC but has no released criterion-specific rules; all-comers gnomAD v4.1 is therefore the default population source.
• Generic calibration supplied for this case: PM2 supporting <= 0.0001, SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020; cited in the case guidance with PMID:25741868).

Sources

Reasoning

The variant is CHEK2 NM_007194.4:c.1247T>C, p.Ile416Thr. The supplied evidence identifies no previously established pathogenic variant producing the same Ile416Thr amino-acid change by another nucleotide substitution. The exact variant is reported in ClinVar as uncertain significance in five clinical-laboratory submissions, not as an established pathogenic variant. No variant-specific literature finding supporting a same-amino-acid pathogenic comparator was available.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinVar variation 449933, exact record NM_007194.4(CHEK2):c.1247T>C (p.Ile416Thr): five clinical-laboratory submissions, all uncertain significance.
• The supplied case evidence contains no established pathogenic same-amino-acid comparator for p.Ile416Thr.

Sources

Reasoning

The target variant is CHEK2 p.Ile416Thr. The supplied PM5 candidate summary reports zero same-residue candidates and zero expert-panel or non-expert-majority pathogenic/likely pathogenic candidates. The exact ClinVar record is uncertain significance, and no established pathogenic different missense substitution at Ile416 is documented in the supplied evidence. Thus the PM5 condition is not fulfilled.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• pm5_candidates.json: total_candidates_seen=0, same_residue_candidates=0, expert_panel_plp_candidates=0, and non_expert_majority_plp_candidates=0.
• ClinVar variation 449933: the exact p.Ile416Thr variant is uncertain significance in five clinical-laboratory submissions.

Sources

Reasoning

The variant is a missense substitution, so the applicable generic PP3/BP4 path is REVEL only; SpliceAI is not used for this missense assessment. REVEL is 0.625, which is below the generic PP3 supporting threshold of >= 0.644 (ClinGen SVI REVEL calibration, Pejaver et al. 2022, PMID:36413997). BayesDel is not usable because no generic ACMG-strength calibration is established. Therefore PP3 is not met.

Rule

Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_007194.4:c.1247T>C is a missense variant, NP_009125.1:p.(Ile416Thr), in exon 11; the missense path uses REVEL only.
• Local REVEL lookup reports 0.625 for NC_000022.11:g.28695722A>G.
• The generic ClinGen SVI REVEL calibration sets PP3 supporting at >=0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997); 0.625 does not reach that threshold.
• BayesDel score 0.247683 was not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

PP5 is not met. The exact-variant ClinVar record NM_007194.4(CHEK2):c.1247T>C (p.Ile416Thr), Variation ID 449933, has five clinical-laboratory submissions, all classified as Uncertain significance, with zero expert-panel submissions. The only validated exact-variant PMID trail is associated with an Ambry Genetics laboratory submission classified as Uncertain significance, not Pathogenic or Likely pathogenic. Therefore no qualifying exact-variant ClinVar expert-panel pathogenic/likely pathogenic classification is available.

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 Variation ID 449933 exactly matches NM_007194.4(CHEK2):c.1247T>C (p.Ile416Thr); its aggregate classification is Uncertain significance with five clinical-laboratory submissions.
• The ClinVar submission audit records zero expert-panel submissions; the only validated exact-variant PMID trail is for an Ambry Genetics submission classified as Uncertain significance.

Sources

Reasoning

BA1 is not met. Generic ACMG/AMP BA1 requires an allele frequency of at least 5%. The default all-comers gnomAD v4.1 data show AF 6.196892630159533e-07 (1/1613712 alleles), with the highest observed subpopulation point estimate 8.477176896641173e-07 in European non-Finnish individuals (1/1179638 alleles). No gnomAD grpmax FAF is reported, but the observed allele frequency is already far below 0.05; therefore BA1 cannot be applied. The CHEK2 VCEP record contains no released criterion-specific rules, so no alternative VCEP population source or threshold governs.

Rule

BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1 all-comers: total AF=6.196892630159533e-07, 1/1613712 alleles, homozygotes=0; highest observed subpopulation was European (non-Finnish), AF=8.477176896641173e-07, 1/1179638 alleles.
• gnomAD v4.1 reports grpmax FAF as null; nevertheless, the observed point frequency is far below the 0.05 BA1 threshold, so a filtering FAF at or above threshold is impossible.
• The CHEK2 specification is listed on CSPEC but has no released criterion-specific rules; generic ACMG/AMP rules therefore govern.
• Generic calibration supplied for this case: BA1 >= 0.05, ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).

Sources

Reasoning

BS1 is not met. The generic rule concerns an allele frequency greater than expected for the disorder, with a supplied default threshold of 1%. The default all-comers gnomAD v4.1 AF is 6.196892630159533e-07 (1/1613712 alleles), and the highest observed subpopulation point estimate is 8.477176896641173e-07 in European non-Finnish individuals; both are far below 0.01. No gnomAD grpmax FAF is reported, so no filtering FAF supports BS1. Because the observed frequency is extremely low rather than elevated, a maximum-credible-frequency exception analysis is not outcome-determinative.

Rule

BS1: Allele frequency is greater than expected for disorder.

Evidence considered

• gnomAD v4.1 all-comers: total AF=6.196892630159533e-07, 1/1613712 alleles; highest observed subpopulation was European (non-Finnish), AF=8.477176896641173e-07, 1/1179638 alleles.
• gnomAD v4.1 reports grpmax FAF as null; the observed frequency is nevertheless far below 0.01, so BS1 is not met on frequency.
• The CHEK2 CSPEC record has no released criterion-specific rules, so the generic BS1 default is used.
• Generic calibration supplied for this case: BS1 >= 0.01; per-gene maximum-credible-frequency derivation is preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

The variant is a missense substitution, so the applicable generic PP3/BP4 path is REVEL only; the SpliceAI score is not substituted for an indeterminate missense REVEL result. REVEL is 0.625, above the generic BP4 supporting threshold of <= 0.29 (ClinGen SVI REVEL calibration, Pejaver et al. 2022, PMID:36413997), and it lies in the REVEL gray zone where neither PP3 nor BP4 is met. BayesDel is not usable because no generic ACMG-strength calibration is established. Therefore BP4 is not met.

Rule

Missense variant -> REVEL only. An indeterminate result on the applicable path means PP3/BP4 are simply not met. It does not license reaching across to the other path's score - a missense variant whose REVEL sits in the gray zone gets no BP4, however clean its SpliceAI delta. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_007194.4:c.1247T>C is a missense variant, NP_009125.1:p.(Ile416Thr), in exon 11; the missense path uses REVEL only.
• Local REVEL lookup reports 0.625 for NC_000022.11:g.28695722A>G.
• The generic ClinGen SVI REVEL calibration sets BP4 supporting at <=0.29 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997); 0.625 does not meet that threshold and is in the indeterminate range.
• SpliceAI max delta 0.016 was not used because splice prediction cannot provide BP4 support for a missense variant under the applicable path.
• BayesDel score 0.247683 was not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

BP6 is not met. The exact-variant ClinVar record NM_007194.4(CHEK2):c.1247T>C (p.Ile416Thr), Variation ID 449933, has five clinical-laboratory submissions, all classified as Uncertain significance, and zero expert-panel submissions. No exact-variant ClinVar expert-panel classification as Benign or Likely benign is present, so ordinary laboratory submissions and the aggregate uncertain-significance label cannot trigger BP6.

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 Variation ID 449933 exactly matches NM_007194.4(CHEK2):c.1247T>C (p.Ile416Thr); the record has five clinical-laboratory submissions, all Uncertain significance.
• The ClinVar submission audit records zero expert-panel submissions and no exact-variant expert-panel Benign or Likely benign classification.

Sources

Reasoning

The available case evidence does not document a de novo occurrence in the proband, confirmed maternity and paternity, absence of family history, or a disease-consistent phenotype. Therefore, the evidence is insufficient to assess PS2.

Rule

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

Evidence considered

• No proband, parental-testing, or family-history evidence relevant to de novo assessment is documented in the available case materials.

Still missing

• Proband-level variant result with confirmed maternity and paternity
• Documented absence of family history
• Disease-consistent phenotype

Reasoning

The exact variant NM_007194.4:c.1247T>C (p.Ile416Thr) lacks documented variant-specific functional assay results in the available evidence. PMID:37449874 is a functional CHEK2 missense-variant study, but its available abstract does not identify this variant, and no full text or assay result for this variant is available. Therefore, the required well-established evidence of a damaging effect cannot be assessed and PS3 is not applied.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. ... Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.

Evidence considered

• Stolarova et al. 2023, PMID:37449874: the available abstract describes a comprehensive functional study of CHEK2 missense variants but does not mention NM_007194.4:c.1247T>C or p.Ile416Thr; no variant-specific result can be extracted.
• The available record does not provide a validated, reproducible, variant-specific in vitro or in vivo assay result for this variant.

Still missing

• Variant-specific functional assay results for CHEK2 c.1247T>C (p.Ile416Thr), including assay validation, controls, biological relevance, and reproducibility, are unavailable.

Sources

Reasoning

The generic PS4 rule requires a significantly increased prevalence in affected individuals, with an OR or RR >5.0 and a confidence interval that does not include 1.0. No case cohort carrying NM_007194.4:c.1247T>C/p.(Ile416Thr), unaffected-control count, matched case frequency, odds ratio, or confidence interval is documented. The literature_pass packet has no ai_classified_papers already read as PS4; the candidate literature reviewed in the packet does not provide exact-variant case-control data. gnomAD v4.1 supplies only a population frequency (1/1,613,712 alleles; AF 6.19689e-7), not an affected-case frequency, so an OR and 95% CI cannot be calculated.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: 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

• gnomAD v4.1 reports 1 alternate allele among 1,613,712 alleles (AF 6.19689e-7), but this is a control-population frequency and cannot substitute for an affected-case frequency.
• literature_pass.json has an empty ai_classified_papers list; the reviewed candidate papers do not establish exact-variant case-control counts, OR/RR, or a confidence interval.

Still missing

• An exact-variant affected cohort and matched unaffected or population-control counts are needed to calculate OR/RR and its 95% CI.

Sources

Reasoning

The variant affects CHEK2 residue Ile416. The authoritative vcep_materials.json domain_tables entry for CHEK2 is absent (domain_tables is empty), and the generic evidence does not establish a qualifying critical functional domain at residue 416 together with absence of benign variation. Cancer Hotspots returned no statistically significant hotspot for CHEK2 I416, and COSMIC returned no result, but those negative findings do not resolve the independent critical-domain route. Therefore PM1 cannot be adjudicated from the supplied evidence.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• vcep_materials.json: domain_tables is empty for CHEK2, so no authoritative approved domain interval can be checked for residue 416.
• Cancer Hotspots query CHEK2 I416: no statistically significant hotspot row found.
• COSMIC query CHEK2 c.1247T>C: no somatic result found.
• The CSPEC record is listed without released criteria; generic ACMG/AMP rules govern this case.

Still missing

• A source establishing the applicable CHEK2 critical functional domains and benign variation within the relevant domain is required.

Sources

Reasoning

The available case evidence does not document an assumed de novo occurrence or parental testing that would establish de novo status without confirmation of maternity and paternity. Therefore, the evidence is insufficient to assess PM6.

Rule

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

Evidence considered

• No parental-testing or assumed-de novo evidence relevant to PM6 is documented in the available case materials.

Still missing

• Evidence that the variant is absent from the available parental samples or otherwise assumed de novo
• Parental-testing details and family-history context

Reasoning

The available case evidence does not identify multiple affected family members, their variant test results, or documented co-segregation with disease. Therefore, PP1 cannot be assessed or assigned a strength.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No family segregation, affected-relative genotype, or informative-meiosis data relevant to PP1 is documented in the available case materials.

Still missing

• Pedigree identifying affected family members
• Variant test results for affected relatives
• Documented co-segregation and number of informative meioses

Reasoning

The available evidence does not provide a gene-level assessment demonstrating both a low rate of benign missense variation in CHEK2 and that missense variants are a common disease mechanism. A single CHEK2 variant is present in gnomAD v4.1 at total allele frequency 6.19689e-07, but that variant-level frequency does not establish the required gene-level missense constraint or disease mechanism. The generic PVS1 context supports loss of function as a mechanism, but does not establish that missense variants are a common mechanism.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• gnomAD v4.1: the individual variant has total AF 6.196892630159533e-07 (1/1613712 alleles), which is not a gene-level missense-rate assessment.
• pvs1_gene_context.json: loss-of-function mechanism is supported, but this does not establish that missense variants are a common disease mechanism.

Still missing

• Gene-level missense constraint/benign-variation analysis and evidence that missense is a common CHEK2 disease mechanism are required.

Sources

Reasoning

The generic PP4 rule requires a patient phenotype or family history highly specific for a disease with a single genetic etiology. The case materials document the exact CHEK2 variant but provide no patient phenotype, cancer diagnosis, age of onset, family history, or other clinical presentation from which disease specificity can be judged. General CHEK2 breast-cancer risk context in the reviewed literature is not a substitute for this patient's phenotype.

Rule

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

Evidence considered

• The case summary contains variant and gene information but no patient-level phenotype or family-history findings.
• The reviewed consensus literature discusses CHEK2 as an intermediate-penetrance breast-cancer gene but does not provide this patient's phenotype or exact-variant clinical presentation.

Still missing

• Patient-level phenotype and family-history details, including the suspected disease diagnosis, are needed.

Sources

Reasoning

BS2 cannot be assessed from the available population data. The generic rule requires observation in a healthy adult individual for a dominant disorder with full penetrance expected at an early age. gnomAD v4.1 contains one heterozygous allele (1/1613712 total alleles) and no homozygotes, but it does not provide a documented healthy-adult phenotype, age, or penetrance assessment for that carrier. CHEK2-related cancer predisposition is not established here as a fully penetrant early-onset disorder, so the population record alone cannot satisfy BS2.

Rule

BS2: Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• gnomAD v4.1 reports one observed allele in the total dataset (1/1613712 alleles), zero homozygotes, and one allele in European non-Finnish individuals; it does not identify the carrier's phenotype or age.
• The CHEK2 CSPEC record lists autosomal-dominant CHEK2-related cancer predisposition but provides no released BS2 rule or penetrance specification.

Still missing

• Documented phenotype and age of the gnomAD carrier are unavailable.
• Full early-age penetrance for the governing CHEK2 disorder is not established for applying BS2.

Sources

Reasoning

The exact variant NM_007194.4:c.1247T>C (p.Ile416Thr) lacks documented variant-specific functional assay results in the available evidence. PMID:37449874 is a functional CHEK2 missense-variant study, but its available abstract does not identify this variant, and no full text or assay result for this variant is available. Therefore, the required well-established evidence of no damaging effect on protein function or splicing cannot be assessed and BS3 is not applied.

Rule

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

Evidence considered

• Stolarova et al. 2023, PMID:37449874: the available abstract describes a comprehensive functional study of CHEK2 missense variants but does not mention NM_007194.4:c.1247T>C or p.Ile416Thr; no variant-specific result can be extracted.
• The available record does not provide a validated, reproducible, variant-specific in vitro or in vivo assay result showing no damaging effect on protein function or splicing.

Still missing

• Variant-specific functional assay results for CHEK2 c.1247T>C (p.Ile416Thr), including assay validation, controls, biological relevance, and reproducibility, are unavailable.

Sources

Reasoning

The available case evidence does not identify affected family members who were tested for the variant, so there is no documented non-segregation. The BS4 phenocopy caveat also cannot be evaluated without family-level phenotype and genotype data.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No affected-relative genotype or family-level non-segregation evidence relevant to BS4 is documented in the available case materials.

Still missing

• Affected relatives with confirmed disease diagnoses
• Variant test results for those affected relatives
• Family-level assessment for phenocopies or more than one pathogenic variant

Reasoning

The available case evidence supports CHEK2 loss of function as a germline disease mechanism, but it does not establish the stronger gene-level proposition that disease-causing variants in CHEK2 are primarily truncating. No quantitative or curated comparison of truncating versus missense disease-causing variants was supplied. Therefore BP1 cannot be applied or excluded from the available evidence.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• pvs1_gene_context.json: CHEK2 loss-of-function mechanism is supported by the targeted germline literature review.
• The supplied evidence does not provide a curated or quantitative demonstration that CHEK2 disease-causing variants are primarily truncating rather than missense.

Still missing

• A curated gene-level assessment showing that CHEK2 disease is caused primarily by truncating variants is required.

Sources

Reasoning

The available evidence does not document this variant in trans with a pathogenic variant in an applicable fully penetrant dominant disorder, or in cis with a pathogenic variant. No parental, offspring, proband-level phase, or affected-proband allelic observation is provided to establish either BP2 path.

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

• No case-level report, pedigree, parental testing, offspring testing, or other validated phasing result documenting a cis or trans relationship with a pathogenic variant was identified in the supplied evidence.

Still missing

• Parental or offspring testing, or other validated phasing evidence, is needed to determine whether NM_007194.4:c.1247T>C is in cis or trans with a pathogenic variant.

Reasoning

The generic BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. The available case materials contain no patient-level case report, alternate molecular diagnosis, or other documented molecular basis that could be evaluated against this exact CHEK2 variant. The absence of such information does not establish BP5.

Rule

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

Evidence considered

• No case-level alternate molecular diagnosis or competing pathogenic molecular finding is documented in the available materials.
• The reviewed literature extracts do not report an exact-variant patient case with an alternate molecular basis.

Still missing

• A documented patient case and confirmed alternate molecular basis for that patient's disease are needed.

Sources