SDHB c.744C>G, p.(Asn248Lys)

Reasoning

PM2 is met at supporting strength because the variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and is exceptionally rare in gnomAD v4.1 (total AF 6.196040234606868e-07; 1/1,613,934 alleles; 0 homozygotes). The observed single allele does not support a strict absent-from-controls claim, so PM2 is limited to supporting strength.

Rule

{'basis': 'generic population threshold fallback because retrieved SDHB CSPEC has no usable criterion-specific rule payload', 'threshold': 'PM2 supporting when population AF is <0.1%, with no homozygotes and no threshold artifact identified'}

Evidence considered

• gnomAD v2.1 and gnomAD-Canada v1.0 report no occurrence of the variant.
• gnomAD v4.1 reports only 1 alternate allele among 1,613,934 total alleles (AF 6.19604e-07), no homozygotes, and a maximum ancestry-specific AF of 8.47489e-07 in European (non-Finnish) individuals.
• Because the variant is observed once in gnomAD v4.1 rather than completely absent from all population datasets, the evidence supports rare-population occurrence at PM2 supporting strength rather than an unqualified absent-from-controls claim.
• The retrieved SDHB CSPEC has no usable criterion-specific PM2 rule payload; the documented generic rare-frequency fallback threshold of <0.1% was applied.

Sources

Reasoning

PP3 is met at supporting strength. NM_003000.3:c.744C>G is a missense variant encoding p.(Asn248Lys), so the missense protein-impact path applies. REVEL is 0.866, exceeding the generic calibrated PP3 threshold of >0.750. The SDHB CSPEC record was reviewed but supplies no PP3/BP4 criterion-specific rule or lookup assignment; therefore, the generic missense rule applies. SpliceAI was not used because it evaluates a different mechanism and cannot support PP3 for this missense substitution.

Rule

Generic ACMG/AMP computational-evidence fallback for missense variants: REVEL >0.750 supports PP3 (supporting); VCEP/CSPEC precedence checked with no PP3/BP4-specific rule available.

Evidence considered

• Variant normalization identifies NM_003000.3:c.744C>G as SDHB p.(Asn248Lys), a missense substitution.
• The SDHB Endocrine Tumor Predisposition CSPEC v1.0 was reviewed; its extracted criteria list and rule payload contain no PP3/BP4-specific instruction or pre-assigned lookup result for this variant.
• The local REVEL lookup reports 0.866 for this variant. Under the applicable generic missense calibration, REVEL >0.750 supports PP3 at supporting strength; the calibrated REVEL thresholds are from the ClinGen SVI computational-evidence calibration publication (PMID:36413997).
• SpliceAI max delta is 0.002, but this splice prediction was deliberately not used because the variant is missense and only the protein-impact path is applicable.

Sources

Reasoning

The case includes a publication reporting SDHB p.N248K, but it describes the same c.744C>G change rather than a different nucleotide substitution producing the same amino-acid change. Therefore, the available report does not satisfy PS1.

Rule

PS1 requires a well-established different nucleotide change that produces the same amino-acid change; an exact report of the case variant does not qualify.

Evidence considered

• PMID:18551016 explicitly reports SDHB c.744C>G, p.N248K in a patient; the reported change is the case variant itself, not an alternate nucleotide change at the same codon.

Still missing

• No independently documented alternate nucleotide change producing p.Asn248Lys was identified in the case evidence.

Sources

Reasoning

The exact ClinVar record has three Likely pathogenic laboratory submissions but no expert-panel submission; therefore it cannot support PP5 under the required exact-variant expert-panel rule.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar variation 428929 exactly matches NM_003000.3:c.744C>G (p.Asn248Lys); its three Likely pathogenic submissions are clinical laboratory submissions, and the submission audit reports zero expert-panel submissions.

Still missing

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

Sources

Reasoning

BA1 is not met. The highest observed gnomAD v4.1 allele frequency is 8.474892284119069e-07 in the European (non-Finnish) population, far below the operational BA1 threshold of >1%; the total frequency is 6.196040234606868e-07.

Rule

{'basis': 'generic population threshold fallback because retrieved SDHB CSPEC has no usable criterion-specific rule payload', 'threshold': 'BA1 requires allele frequency >1%'}

Evidence considered

• gnomAD v4.1 reports 1 alternate allele among 1,613,934 total alleles (AF 6.19604e-07; 0 homozygotes). The highest reported ancestry-specific frequency is in European (non-Finnish): 1/1,179,956 alleles (AF 8.47489e-07; 0 homozygotes). These frequencies are many orders of magnitude below the BA1 threshold of >1%.
• The SDHB ClinGen specification was reviewed first, but its retrieved rule payload is empty and framework_complete is false; therefore no usable SDHB-specific BA1 threshold was available and the documented generic operational threshold was used.

Sources

Reasoning

BS1 is not met. The variant is far below the operational BS1 threshold of >0.3% in every reported population; gnomAD v4.1 total AF is 6.196040234606868e-07 and the highest ancestry-specific AF is 8.474892284119069e-07.

Rule

{'basis': 'generic population threshold fallback because retrieved SDHB CSPEC has no usable criterion-specific rule payload', 'threshold': 'BS1 requires allele frequency >0.3%'}

Evidence considered

• gnomAD v4.1 reports a maximum observed frequency of 8.47489e-07 in European (non-Finnish) individuals, with 0 homozygotes; total AF is 6.19604e-07.
• The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0. Neither the observed rare frequency nor the absence in those datasets approaches a benign-frequency threshold of >0.3%.
• The retrieved SDHB CSPEC is incomplete for criterion-level rules, so the documented generic operational BS1 threshold was used.

Sources

Reasoning

BP4 is not met. This missense variant must be evaluated only with the protein-impact path; its REVEL score of 0.866 is not below the generic calibrated BP4 threshold of <0.250. The low SpliceAI score is not evidence for BP4 because no predicted splice impact does not address the effect of the Asn-to-Lys substitution.

Rule

Generic ACMG/AMP computational-evidence fallback for missense variants: REVEL <0.250 supports BP4 (supporting); VCEP/CSPEC precedence checked with no PP3/BP4-specific rule available.

Evidence considered

• Variant normalization identifies NM_003000.3:c.744C>G as SDHB p.(Asn248Lys), a missense substitution.
• The SDHB Endocrine Tumor Predisposition CSPEC v1.0 was reviewed; its extracted criteria list and rule payload contain no PP3/BP4-specific instruction or pre-assigned lookup result for this variant.
• The local REVEL lookup reports 0.866, which does not meet the applicable generic missense BP4 threshold of REVEL <0.250. The calibrated REVEL thresholds are from the ClinGen SVI computational-evidence calibration publication (PMID:36413997).
• SpliceAI max delta is 0.002, but this splice prediction was deliberately not used because the variant is missense and only the protein-impact path is applicable.

Sources

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign classification is present; BP6 cannot be applied.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar variation 428929 exactly matches NM_003000.3:c.744C>G (p.Asn248Lys); all three listed laboratory submissions are Likely pathogenic and the submission audit reports zero expert-panel submissions.

Still missing

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

Sources

Reasoning

No case-specific evidence documents that NM_003000.3:c.744C>G (p.Asn248Lys) occurred de novo in the proband. The available variant report identifies an affected individual but does not provide parental genotypes, maternity/paternity confirmation, or testing demonstrating absence of the variant in both parents.

Evidence considered

• PMID:18551016 reports the variant in one patient with a left pneumogastric-nerve head-and-neck paraganglioma, but the extracted report contains no parental testing or de novo analysis.
• The SDHB ClinGen specification is present, but its case bundle contains no criterion-specific PS2 rule payload; no usable SDHB-specific de novo threshold was available.

Still missing

• Parental testing results for both biological parents are not available.
• Confirmation of maternity and paternity is not available.
• The proband's de novo status is not documented.

Sources

Reasoning

No validated variant-specific functional assay demonstrating a damaging effect of SDHB c.744C>G (p.Asn248Lys) was identified. PMID:18551016 reports the variant in a patient but describes clinical genetic screening rather than a functional assay. PMID:15989954 provides structural context for SDHB/Complex II but does not test p.Asn248Lys, and PMID:25720320 reports SDHB immunohistochemistry at the tumor/cohort level without identifying this variant. Therefore PS3 cannot be applied.

Evidence considered

• The SDHB VCEP/ClinGen specification is present, but its extracted ruleset contains no explicit PS3 calibration or usable criterion-specific rule payload.
• PMID:18551016 explicitly reports SDHB c.744C>G (p.N248K) in one patient, but the reported methods are genetic screening methods and no functional assay result for the variant is provided.
• PMID:15989954 reports a porcine Complex II crystal structure and SDHB iron-sulfur-cluster structural context, but does not mention or test p.Asn248Lys.
• PMID:25720320 reports SDHB/SDHA immunohistochemistry in a multicenter tumor cohort, including tumors with SDHB mutations, but does not identify c.744C>G/p.N248K or provide variant-specific assay results.

Still missing

• A validated assay measuring SDHB/Complex II function for p.Asn248Lys is not available in the reviewed evidence.
• No variant-specific assay controls, replicate data, or quantitative comparison with wild-type and known pathogenic/benign controls were identified.

Sources

Reasoning

One published individual with the exact variant is reported, but no case-control comparison, affected-cohort denominator for this variant, control count, or statistical enrichment analysis is available; PS4 cannot be assessed as met.

Rule

Generic ACMG/AMP PS4: increased prevalence in affected individuals compared with controls requires case-control enrichment evidence.

Evidence considered

• PMID:18551016 reports SDHB c.744C>G (p.N248K) in one Caucasian patient with a left pneumogastric paraganglioma; the paper's broader cohort data do not provide variant-specific enrichment versus controls.
• The SDHB CSPEC framework was reviewed first; its retrieved rule payload contains no criterion-specific PS4 instruction, so generic ACMG/AMP PS4 evidence requirements were used.

Still missing

• Variant-specific case-control or appropriately ascertained affected-cohort data with control frequency and statistical enrichment are needed.

Sources

Reasoning

The governing SDHB CSPEC framework is present, but its extracted rule payload is unstructured and vcep_materials.json has no domain_tables entry for SDHB. The available structural paper places the C-terminal SDHB iron-sulfur subunit domain at residues B115-B247; the variant is at residue 248, immediately outside that reported boundary. No authoritative approved critical-domain or hotspot designation covering N248 is available in the bundle, so PM1 cannot be assigned.

Rule

Use the governing VCEP domain table when present; absent an authoritative approved critical-domain or hotspot designation covering the residue, PM1 cannot be assigned.

Evidence considered

• The SDHB CSPEC is the governing framework, but the bundle reports framework_complete=false, rule_payload={}, and domain_tables={}.
• PMID:15989954 describes the SDHB iron-sulfur subunit C-terminal domain as B115-B247; N248 is not within that stated structural domain boundary.
• The case hotspot search reported no statistically significant hotspot, but no hotspots key is present in source_registry for citation.

Still missing

• The governing CSPEC domain/hotspot specifications were not available as structured rules or a domain table.
• Human review is needed to determine whether the governing VCEP document contains an approved critical region that includes residue 248 despite the absent extracted domain table.

Sources

Reasoning

The applicable SDHB ClinGen specification identifies autosomal dominant hereditary pheochromocytoma-paraganglioma but provides no usable PM3 rule payload. The variant was reported in one affected individual with a paraganglioma, but the available report does not establish a second pathogenic SDHB variant, phase in trans, biallelic state, or a recessive disease context. PM3 therefore cannot be assessed from the available evidence.

Evidence considered

• The SDHB ClinGen specification (Version 1.0) lists autosomal dominant inheritance for hereditary pheochromocytoma-paraganglioma, but its supplied rule payload contains no PM3-specific instructions.
• PMID:18551016 reports SDHB c.744C>G (p.N248K) in one patient with a left pneumogastric-nerve paraganglioma and also reports an SDHB 5′-UTR change c.1-36T>C; the available extraction does not establish that the two changes are pathogenic alleles in trans or otherwise demonstrate biallelic disease.

Still missing

• No documented pathogenic or likely pathogenic variant in the same individual for evaluation in trans.
• No phasing information establishing cis or trans configuration with another SDHB variant.
• No evidence supporting a recessive/biallelic SDHB disease model for this case.

Sources

Reasoning

No alternate pathogenic missense variant at SDHB residue 248 was identified in the provided evidence. PMID:18551016 reports p.N248K itself, not a different amino-acid substitution at residue 248, and pm5_candidates.json contains no candidates. The case therefore lacks a qualifying comparator for PM5.

Rule

PM5 requires a pathogenic missense change at the same residue that is different from the variant under assessment; the exact same variant is not a PM5 comparator.

Evidence considered

• PMID:18551016 reports p.N248K, the case amino-acid change, and does not report a different missense substitution at residue 248.
• pm5_candidates_summary reports zero same-residue candidates and instructs that PM5 must not be applied from that artifact alone.

Still missing

• A complete curated search for independently established pathogenic alternate missense substitutions at residue 248 is not available in the bundle.
• The exact SDHB VCEP PM5 rule is unavailable in structured form.

Sources

Reasoning

No case-specific evidence supports presumed de novo occurrence without parental testing. The available report does not state that the variant was presumed de novo or provide a clinical basis for that presumption.

Evidence considered

• PMID:18551016 identifies the variant in an affected patient but does not report parental testing or describe the variant as presumed de novo.
• The SDHB ClinGen specification is incomplete in the supplied bundle and provides no usable criterion-specific PM6 rule payload.

Still missing

• No documented presumed-de-novo assessment is available.
• Parental genotypes and relevant family history are unavailable.
• The proband's phenotype and the circumstances supporting a presumed-de-novo conclusion require primary-record review.

Sources

Reasoning

The available evidence documents one affected individual with the variant but does not provide affected relatives, informative meioses, phase, or a cosegregation analysis. Therefore, supportive segregation evidence cannot be assigned.

Evidence considered

• PMID:18551016 reports the variant in one 49-year-old man with a left pneumogastric-nerve head-and-neck paraganglioma and does not report affected relatives or cosegregation data.
• The same report describes a Belgian cohort of unrelated patients; cohort-level identification of SDHB mutations is not segregation evidence for this variant.
• The SDHB ClinGen specification is present but incomplete in the supplied case bundle and contains no usable criterion-specific PP1 rule payload.

Still missing

• No family pedigree or number of informative meioses is available.
• No genotypes and phenotypes for affected relatives are available.
• No segregation likelihood analysis or family-level cosegregation result is available.

Sources

Reasoning

The bundle supports SDHB loss of function as a disease mechanism but does not establish that missense variation is a common pathogenic mechanism for SDHB or provide the gene-level missense proportion required for PP2. The available CSPEC extraction contains no PP2 rule.

Rule

PP2 requires gene-specific evidence that missense variants are a common pathogenic mechanism; loss-of-function mechanism evidence alone is insufficient.

Evidence considered

• The SDHB CSPEC framework extraction contains no structured criterion rules, including no PP2 specification.
• The case materials support an SDHB loss-of-function disease mechanism, which is not by itself evidence that missense variation is the predominant pathogenic mechanism.

Still missing

• No applicable SDHB-specific PP2 rule was available.
• No validated gene-level analysis showing a high proportion of pathogenic SDHB missense variants was provided.

Sources

Reasoning

The reported variant carrier had a vagal head-and-neck paraganglioma, but the supplied evidence does not establish that this phenotype is sufficiently specific for SDHB-related hereditary pheochromocytoma-paraganglioma to apply PP4, nor does it provide phenotype data for the case being classified.

Rule

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

Evidence considered

• PMID:18551016 identifies the exact variant in a patient with a left pneumogastric paraganglioma, but this single observation does not demonstrate phenotype specificity for SDHB.
• The reviewed SDHB CSPEC identifies hereditary pheochromocytoma-paraganglioma as the disease context but provides no retrieved PP4-specific rule or phenotype threshold.

Still missing

• Case-specific clinical phenotype, family history, tumor features, and exclusion of alternative hereditary pheochromocytoma-paraganglioma causes are needed.
• A phenotype-specificity framework or data demonstrating that the observed phenotype is highly specific for SDHB-related disease are needed.

Sources

Reasoning

BS2 cannot be assessed from the available population data. gnomAD reports one heterozygous allele and no homozygotes, but does not establish that a carrier is an older unaffected adult or provide phenotype and penetrance information sufficient for BS2. No healthy homozygote or clearly unaffected carrier observation was identified in the case bundle.

Rule

{'basis': 'BS2 requires reliable observation in unaffected adults, typically including homozygotes or multiple unaffected heterozygotes; population allele counts alone are insufficient', 'threshold': 'No phenotype-confirmed unaffected individual observation available'}

Evidence considered

• gnomAD v4.1 reports 1 alternate allele among 1,613,934 alleles and 0 homozygotes; the dataset record alone does not provide the clinical phenotype, age, or ascertainment needed to treat the carrier as an unaffected individual for BS2.
• The retrieved SDHB ClinGen specification identifies autosomal dominant hereditary pheochromocytoma-paraganglioma but contains no usable BS2 rule payload or penetrance-specific guidance.

Still missing

• No phenotype-confirmed healthy adult carrier data for this variant
• No documented unaffected homozygote observation
• No SDHB-specific penetrance-adjusted BS2 rule was retrieved from the incomplete CSPEC

Sources

Reasoning

No validated variant-specific functional assay demonstrating preserved SDHB function for SDHB c.744C>G (p.Asn248Lys) was identified. The available exact-variant publication is a clinical genetic screening report without functional testing, while the structural and immunohistochemistry publications provide only non-variant-specific context. Consequently, BS3 cannot be applied.

Evidence considered

• The SDHB VCEP/ClinGen specification is present, but its extracted ruleset contains no explicit BS3 calibration or usable criterion-specific rule payload.
• PMID:18551016 reports the exact p.N248K variant in a patient but does not report a functional assay showing retained function.
• PMID:15989954 characterizes Complex II structure and SDHB subunit domains but does not evaluate p.Asn248Lys or establish a benign functional result.
• PMID:25720320 evaluates SDHB immunohistochemistry across a tumor cohort without reporting this variant or any variant-specific normal-function result.

Still missing

• A validated assay demonstrating normal SDHB/Complex II function for p.Asn248Lys is not available in the reviewed evidence.
• No variant-specific benign control comparison, assay validation, or reproducible quantitative functional result was identified.

Sources

Reasoning

No informative unaffected relatives carrying the variant are reported. The available publication provides no family segregation data, no tested unaffected relatives, and no age or clinical assessment sufficient to establish non-segregation.

Evidence considered

• PMID:18551016 reports one affected carrier and does not describe any unaffected carrier relatives or non-segregation findings.
• The absence of reported family data cannot establish BS4.

Still missing

• No unaffected relatives with confirmed carrier status are documented.
• No family pedigree, penetrance assessment, or age-appropriate clinical evaluation is available.
• No non-segregation analysis is available.

Sources

Reasoning

No SDHB-specific evidence was provided showing that missense variants are a benign mechanism or that SDHB has a low rate of pathogenic missense variation. The available CSPEC extraction contains no BP1 rule, so BP1 cannot be assigned.

Rule

BP1 requires gene-specific evidence that missense variation is generally a benign mechanism; absence of such evidence is insufficient for BP1.

Evidence considered

• The SDHB CSPEC framework extraction contains no structured criterion rules, including no BP1 specification.
• The available case evidence does not establish a low rate of pathogenic SDHB missense variants.

Still missing

• No applicable SDHB-specific BP1 rule was available.
• No validated gene-level missense constraint or pathogenicity distribution analysis supporting BP1 was provided.

Sources

Reasoning

The applicable SDHB ClinGen specification provides no usable BP2 rule payload. Available case evidence does not show this variant in trans with a pathogenic variant in an affected individual, nor does it provide sufficient phase and pathogenicity data to establish a benign allelic configuration. BP2 cannot be assessed.

Evidence considered

• The SDHB ClinGen specification (Version 1.0) lists autosomal dominant inheritance for hereditary pheochromocytoma-paraganglioma, but its supplied rule payload contains no BP2-specific instructions.
• PMID:18551016 reports p.N248K together with an SDHB 5′-UTR change in one patient, but the available extraction does not establish phase, demonstrate that the changes are in trans, or classify the second change as pathogenic.

Still missing

• No affected individual is documented with this variant and a separately established pathogenic variant in trans.
• No reliable phase information for the reported SDHB 5′-UTR change c.1-36T>C.
• No evidence establishing the second reported change as pathogenic and suitable for BP2 assessment.

Sources

Reasoning

No evidence identifies an alternative molecular diagnosis that fully explains the phenotype in a carrier of this exact variant; BP5 cannot be assessed as met.

Rule

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

Evidence considered

• The consolidated evidence bundle contains no case-specific alternate molecular diagnosis or dual-diagnosis finding for this variant.

Still missing

• Case-specific phenotype and molecular testing results demonstrating an alternative diagnosis that fully explains the clinical presentation are needed.