STK11 c.369G>A, p.(Gln123=)

Reasoning

BA1 is met under the generic population threshold (>1% allele frequency in any population). The exact variant NM_000455.4:c.369G>A is present in gnomAD v4.1 at overall AF 0.114% and in the African/African American population at AF 2.117% (1,589/75,054 alleles; 23 homozygotes). The African/African American frequency exceeds 1%; the same elevated population frequency is also observed in gnomAD v2.1 and gnomAD-Canada, reducing concern that this is a single-dataset artifact.

Rule

Generic ACMG/AMP population rule: BA1 at allele frequency >1% in any population; use the highest adequately sampled population frequency and consider ancestry-specific frequency artifacts.

Evidence considered

• gnomAD v4.1 reports NM_000455.4:c.369G>A / 19-1218495-G-A at overall AF 0.0011403893685961559 (1,840/1,613,484 alleles) and African/African American AF 0.021171423241932476 (1,589/75,054 alleles; 23 homozygotes).
• gnomAD v2.1 reports overall AF 0.002011426615025785 and African/African American AF 0.021255479282110662 (514/24,182 alleles; 7 homozygotes).
• gnomAD-Canada v1.0 reports AF 0.0016835016835016834 (31/18,414 alleles; 1 homozygote); its African population AF is 0.028431372549019607 (29/1,020 alleles; 1 homozygote).
• Generic population threshold applied: BA1 is met when the allele frequency exceeds 1% in any population; the highest observed population frequency is approximately 2.1% to 2.8% in African/African American samples.

Sources

Reasoning

BS1 is met under the generic population threshold (>0.3% allele frequency). The exact variant is present above 0.3% overall in gnomAD v2.1 (0.201% does not exceed the threshold) only when considering the newer gnomAD v4.1 overall AF of 0.114% it remains below 0.3%; however, the African/African American population frequency is 2.117% in gnomAD v4.1 and 2.126% in gnomAD v2.1, and gnomAD-Canada reports 2.843% in its African population. Thus BS1 is met based on a well-represented ancestry-specific frequency, not the pooled frequency. The finding is concordant across datasets and includes homozygotes.

Rule

Generic ACMG/AMP population rule: BS1 at allele frequency >0.3% in an appropriately represented population; ancestry-specific frequencies may be used when the population sample is sufficiently large and the signal is concordant.

Evidence considered

• gnomAD v4.1 reports African/African American AF 0.021171423241932476 (1,589/75,054 alleles; 23 homozygotes), well above 0.003.
• gnomAD v2.1 reports African/African American AF 0.021255479282110662 (514/24,182 alleles; 7 homozygotes), well above 0.003.
• gnomAD-Canada v1.0 reports African population AF 0.028431372549019607 (29/1,020 alleles; 1 homozygote), also above 0.003.
• The pooled frequencies are lower (gnomAD v4.1 0.114%, gnomAD v2.1 0.201%, and gnomAD-Canada 0.168%), so this call relies specifically on the reproducible ancestry-specific maximum rather than an inflated pooled estimate.
• Generic population threshold applied: BS1 at allele frequency >0.3% in an appropriately represented population.

Sources

Reasoning

This is a synonymous substitution, not a missense change, so REVEL/BayesDel (missense-path predictors) do not apply and are not usable here regardless of score (REVEL and BayesDel both returned score=null/not found in prefetch for this variant, and BayesDel additionally lacks any pipeline-verified published threshold). Per the generic ACMG fallback in-silico calibration table (used because no STK11 VCEP-specific PP3/BP4 spreadsheet was retrieved), non-missense variants are assessed via SpliceAI alone. SpliceAI max delta = 0.003, well under the <0.1 threshold for BP4 (supporting), so BP4 is met.

Rule

generic_acmg_combination_rules: SpliceAI max delta < 0.1 -> BP4 (supporting), applied to non-missense variant types

Evidence considered

• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.003).
• Generic ACMG fallback rule: SpliceAI max delta < 0.1 -> BP4 (supporting) for non-missense (synonymous/intronic/non-canonical-splice-position) variants.
• REVEL score not found (null) and BayesDel score not found (null) in prefetch for this variant; in any case both are missense-path predictors inapplicable to this synonymous variant, and BayesDel additionally has no verified published calibration threshold available to this pipeline.

Sources

Reasoning

PM2 is not met because the exact variant is clearly present in population databases. gnomAD v4.1 reports 1,840 alternate alleles and 25 homozygotes overall; gnomAD v2.1 reports 564 alternate alleles and 7 homozygotes; and gnomAD-Canada reports 31 alternate alleles and 1 homozygote. The overall frequencies are approximately 0.114%, 0.201%, and 0.168%, respectively, all nonzero and above the generic PM2 rarity threshold of <0.1% in this framework; the much higher African/African American frequency further excludes rarity.

Rule

Generic ACMG/AMP population rule: PM2 requires absence or frequency below 0.1% in population databases; any clear recurring observation at higher frequency prevents PM2.

Evidence considered

• gnomAD v4.1: AF 0.0011403893685961559 (1,840/1,613,484 alleles), 25 homozygotes.
• gnomAD v2.1: AF 0.002011426615025785 (564/280,398 alleles), 7 homozygotes.
• gnomAD-Canada v1.0: AF 0.0016835016835016834 (31/18,414 alleles), 1 homozygote.
• Generic population threshold applied: PM2 requires absence or a sufficiently rare frequency below 0.1%; this variant is observed repeatedly and exceeds that threshold in the pooled gnomAD datasets.

Sources

Reasoning

NM_000455.4:c.369G>A is a synonymous variant (NP_000446.1:p.(Q123=)); no VCEP-specific CSPEC was retrieved for STK11 (cspec.found=false), so the generic ACMG fallback in-silico rule table applies. For non-missense (synonymous/intronic/non-canonical splice) variants that table specifies using SpliceAI alone: SpliceAI max delta = 0.003 (DS_AG=0.003, DS_AL=0.0, DS_DG=0.002, DS_DL=0.001), far below the >0.2 threshold required for PP3. PP3 is therefore not met.

Rule

generic_acmg_combination_rules: SpliceAI max delta > 0.2 -> PP3 (supporting), applied to non-missense variant types

Evidence considered

• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.003, all four DS_* sub-scores <=0.003).
• Generic ACMG fallback rule (this lab's in-silico calibration table, output/generic_acmg_classification_rules.md) specifies SpliceAI max delta > 0.2 for PP3 in non-missense variants; observed delta is well below this threshold.
• No STK11-specific VCEP CSPEC or PP3/BP4 lookup spreadsheet was retrieved for this case (vcep_materials.json: no cspec url available, summaries empty), so generic fallback governs.

Sources

Reasoning

PP5 is not met. The exact-variant ClinVar record has no expert-panel submission (expert_panel_submissions = 0); its Benign/Likely benign classifications are from ordinary laboratory submissions and aggregate ClinVar data. These assertions are explicitly excluded from PP5 and cannot provide pathogenic support.

Evidence considered

• The exact-variant ClinVar record NM_000455.5(STK11):c.369G>A (p.Gln123=), ClinVar variation 141198, reports Benign/Likely benign laboratory submissions and no expert-panel submissions.
• Because no exact-variant expert-panel Pathogenic or Likely pathogenic classification exists, the PP5 trigger is absent; ordinary laboratory submissions and aggregate ClinVar labels were not used to apply PP5.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is present.

Sources

Reasoning

BP6 is not met under the required rule. Although the exact-variant ClinVar record contains Benign/Likely benign laboratory submissions, it has no exact-variant ClinVar expert-panel benign assertion (expert_panel_submissions = 0). Ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions cannot trigger BP6.

Evidence considered

• The exact-variant ClinVar record (variation 141198) reports Benign/Likely benign classifications from laboratory submissions but no expert-panel submission.
• The available benign aggregate and non-expert laboratory assertions are explicitly insufficient for BP6 under the specified rule.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present.

Sources

Reasoning

No case-specific proband and parental testing data are provided for NM_000455.4:c.369G>A. The evidence bundle contains no confirmed de novo observation, parental genotypes, maternity/paternity confirmation, or mosaicism assessment; therefore PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with maternity and paternity confirmed; strength depends on phenotype specificity and confirmation details.

Evidence considered

• The case summary identifies the variant as NM_000455.4:c.369G>A in STK11 but does not provide a proband-level de novo observation or parental testing result.
• The consolidated evidence bundle contains no case-specific pedigree, meiosis count, parental genotype, or de novo testing evidence for this variant.

Still missing

• Proband genotype and phenotype-linked case report or laboratory record
• Confirmed parental genotypes showing absence of the variant in both parents
• Maternity/paternity confirmation and assessment for parental mosaicism, if applicable

Reasoning

No gene-specific VCEP/CSPEC was found for STK11 (framework_mode: generic_acmg, cspec.found=false), so generic ACMG/AMP applies. No functional assay data (kinase activity assays, minigene/RNA splicing assays, complementation assays, or other validated functional studies) for NM_000455.4:c.369G>A (p.(Gln123=)) was present anywhere in the case bundle: source_registry, prefetch, evidence, literature_pass, and fulltext_map contain only ACMG/AMP guideline and secondary-findings policy papers (PMIDs 25741868, 25356965, 25394175, 26389210, 26389258, 27854360, 28492532), none of which report an experimental functional assay of this variant. There is therefore no evidence to support PS3.

Still missing

• No published functional/splicing assay (e.g., minigene splicing assay, kinase activity assay) identified for NM_000455.4:c.369G>A or the resulting synonymous change p.(Gln123=).
• No VCEP-specific PS3 assay validation criteria available for STK11 in this case bundle.

Reasoning

No case-control study, statistically significant case enrichment, or adequately characterized affected-case series for the exact variant NM_000455.4:c.369G>A was provided. The available ClinVar record is an aggregate of laboratory submissions and is not case-control evidence; no PS4 conclusion can be inferred from its benign classification.

Evidence considered

• The consolidated bundle contains no exact-variant case-control dataset or statistical enrichment analysis.
• ClinVar reports aggregate Benign/Likely benign laboratory submissions for the exact variant, but aggregate laboratory classifications are not PS4 case-control evidence.

Still missing

• Exact-variant case counts, control counts, enrichment statistics, and study methodology are unavailable.
• No adequately documented affected-case series for the exact variant is available in the bundle.

Reasoning

No applicable STK11 VCEP/ClinGen specification was available, so the generic ACMG/AMP framework was used. The evidence bundle contains no affected-proband observations, second pathogenic/likely pathogenic allele, phase information, or documented biallelic/compound-heterozygous inheritance for NM_000455.4:c.369G>A (NP_000446.1:p.(Gln123=)). PM3 therefore cannot be assessed.

Rule

Generic ACMG/AMP PM3: apply only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual, with strength determined by the number and quality of independent observations and phase evidence.

Evidence considered

• The governing materials report that no STK11 ClinGen/VCEP specification was found and that generic ACMG/AMP fallback applies.
• The consolidated case-evidence bundle provides no phase, affected-proband, second-allele, or inheritance observations relevant to PM3.

Still missing

• Affected-proband case data with a pathogenic or likely pathogenic variant in trans are not available.
• Parental testing or other phase information is not available.
• Inheritance mode and evidence for biallelic/compound-heterozygous disease are not documented.

Reasoning

No case-specific report of NM_000455.4:c.369G>A as apparently de novo is available. Parental testing and maternity/paternity confirmation are absent, so PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in a patient with the disease, but without confirmation of paternity and maternity; this is weaker than PS2.

Evidence considered

• The evidence bundle does not document an apparently de novo occurrence of NM_000455.4:c.369G>A in an affected individual.
• No parental genotype results or family-history details are available to support an assumed de novo event.

Still missing

• A publication or clinical record describing this exact variant in an affected proband
• Parental testing demonstrating absence of the variant
• Confirmation of maternity and paternity

Reasoning

No informative affected or unaffected relatives, genotype-phenotype observations, or meioses are reported for NM_000455.4:c.369G>A. Consequently, cosegregation cannot be evaluated and PP1 cannot be assessed.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength may increase with multiple informative meioses.

Evidence considered

• The consolidated case-evidence bundle contains no family pedigree, relative-level phenotype information, relative genotypes, or informative meiosis count for this variant.
• Population observations and ClinVar classifications do not constitute cosegregation evidence and were not used for PP1.

Still missing

• Pedigree with affected and unaffected relatives
• Genotypes for informative relatives
• Phenotype status and diagnostic criteria for each relative
• Number of informative meioses and segregation results

Reasoning

The case bundle does not provide the patient's phenotype, diagnostic findings, or a clinical assessment establishing a highly specific phenotype for a Peutz-Jeghers syndrome spectrum disorder. Conditions listed in ClinVar are assertion context rather than patient phenotype and cannot establish PP4.

Evidence considered

• No patient-level phenotype or syndrome-specific clinical findings are present in the consolidated case-evidence bundle.
• ClinVar condition labels include Peutz-Jeghers syndrome, but database condition labels do not document this patient's phenotype and were not used to apply PP4.

Still missing

• Patient phenotype and diagnostic findings are unavailable.
• No evidence establishes that the patient's phenotype is highly specific for STK11-related disease.

Reasoning

The variant has 25 homozygotes in gnomAD v4.1, 7 homozygotes in gnomAD v2.1, and 1 homozygote in gnomAD-Canada. This is potentially relevant to BS2 for a highly penetrant autosomal-dominant condition, but the available population databases do not establish that these individuals are clinically unaffected, do not provide phenotype/age-of-onset ascertainment sufficient for this criterion, and may include individuals with unrecognized disease or reduced penetrance. Therefore homozygote counts alone are insufficient to adjudicate BS2.

Rule

Generic ACMG/AMP BS2 requires observation in healthy individuals, including homozygotes for a dominant condition; population-database homozygote counts without phenotype and age/penetrance ascertainment are insufficient.

Evidence considered

• gnomAD v4.1 reports 25 homozygotes overall, including 23 in the African/African American population.
• gnomAD v2.1 reports 7 homozygotes overall, including 7 in the African/African American population.
• gnomAD-Canada v1.0 reports 1 homozygote overall, including 1 in its African population.
• Homozygote observations from an ostensibly population-based database are not equivalent to documented unaffected individuals without phenotype, age, ascertainment, and penetrance information.

Still missing

• No phenotype-confirmed, adequately aged unaffected homozygote individuals are documented.
• No source establishes that the relevant population-database participants were screened for STK11-related Peutz-Jeghers syndrome or had sufficient age and penetrance context to qualify as unaffected individuals.

Sources

Reasoning

No gene-specific VCEP/CSPEC was found for STK11 (framework_mode: generic_acmg, cspec.found=false), so generic ACMG/AMP applies. No functional assay data demonstrating normal/wild-type activity (e.g., kinase activity assay showing no functional impact, splicing reporter assay showing normal splicing) for NM_000455.4:c.369G>A was present anywhere in the case bundle. The candidate PMIDs identified by literature triage (25741868, 25356965, 25394175, 26389210, 26389258, 27854360, 28492532) are all ACMG/AMP methodology or secondary-findings policy statements, not functional characterization studies of this variant. There is therefore no evidence to support BS3.

Still missing

• No published functional assay (splicing minigene, kinase activity assay) demonstrating normal/benign functional impact for this variant was identified.
• SpliceAI in silico screening (screenshots/prefetch) is not a validated functional assay and cannot be used for BS3.

Reasoning

No affected relatives who lack NM_000455.4:c.369G>A are documented, and no family segregation study is available. Therefore lack of segregation cannot be established and BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in an affected family member; application requires an informative family study and consideration of phenocopies, reduced penetrance, and age-dependent disease expression.

Evidence considered

• The evidence bundle provides no affected-relative genotype/phenotype comparisons or documented non-segregation for this variant.
• Absence of family data is insufficient to apply BS4; no unaffected or affected relative result was treated as evidence of non-segregation.

Still missing

• Affected relatives assessed for the variant
• Reliable phenotype classification for those relatives
• Genotype results demonstrating non-segregation
• Assessment of phenocopies, reduced penetrance, and age-dependent expression

Reasoning

No applicable STK11 VCEP/ClinGen specification was available, so the generic ACMG/AMP framework was used. The evidence bundle contains no documented observation of NM_000455.4:c.369G>A in trans with a pathogenic/likely pathogenic variant in a dominant disorder or in cis with a pathogenic/likely pathogenic variant in a recessive disorder. BP2 cannot be assessed from the available evidence.

Rule

Generic ACMG/AMP BP2: apply when the variant is observed in trans with a pathogenic/likely pathogenic variant in a dominant disorder or in cis with a pathogenic/likely pathogenic variant in a recessive disorder; phase and inheritance model must be established.

Evidence considered

• The governing materials report that no STK11 ClinGen/VCEP specification was found and that generic ACMG/AMP fallback applies.
• The consolidated case-evidence bundle provides no cis/trans phase, affected-proband, pathogenic-partner-variant, or inheritance observations relevant to BP2.

Still missing

• No affected or unaffected individual-level genotype data establish cis or trans phase with a pathogenic/likely pathogenic variant.
• No parental or family segregation data are available.
• The relevant inheritance model for a BP2 observation is not documented.

Reasoning

No patient-level molecular diagnosis of an alternative condition is documented, and no evidence shows that an alternative molecular etiology explains the patient's phenotype. The available ClinVar classification and population observations do not establish BP5.

Evidence considered

• The consolidated bundle contains no patient-level alternative pathogenic variant or molecular diagnosis that could explain the clinical presentation.
• ClinVar aggregate classification and population frequency data were not treated as evidence of an alternative molecular etiology.

Still missing

• Patient phenotype and clinical indication are unavailable.
• No independent molecular diagnosis providing an alternative explanation is documented.

Reasoning

BP7 requires both (a) splicing prediction algorithms show no impact to the splice consensus or new splice site creation, and (b) the nucleotide is not highly conserved. Criterion (a) is satisfied by the same SpliceAI evidence already credited under BP4 (max delta 0.003). No nucleotide-conservation metric (e.g. phyloP, GERP) was found anywhere in the evidence bundle for this variant, so criterion (b) cannot be verified. To avoid double-counting the identical SpliceAI-derived splice-impact evidence under both BP4 and BP7 for the same variant, and because the conservation component of BP7 remains unverified, BP7 is left not_assessed rather than independently applied.

Evidence considered

• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.003), satisfying the splice-impact prong of BP7, but no conservation data was located to satisfy the second required prong.

Still missing

• No nucleotide conservation score (phyloP, GERP, or equivalent) is present in the evidence bundle for c.369G>A; needed to confirm the low-conservation prong of BP7.
• No STK11 VCEP-specific PP3/BP4/BP7 lookup table was retrieved to check for a gene-specific pre-assigned BP7 code.

Sources