SDHB c.434A>G, p.Asn145Ser

Reasoning

The variant is absent from gnomAD v2.1 and occurs only once in gnomAD v4.1: total AF 6.246080584433268e-07 (1/1601004 alleles), with zero homozygotes. This is below the supplied generic PM2 supporting threshold of 0.0001. The v4.1 record is the default all-comers source because no released SDHB criterion specifies a non-cancer or exome-only source.

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: variant absent.
• gnomAD v4.1: total AF=6.246080584433268e-07, 1/1601004 alleles, homozygotes=0.
• The supplied generic PM2 calibration threshold is <=0.0001 for supporting strength (ClinGen SVI recommendation, identified in the case instructions with PMID:25741868).
• The SDHB CSPEC entry is present but has no released criteria; therefore no non-cancer or exome-only source override applies in this case.

Sources

Reasoning

The variant is a missense substitution, NM_003000.3:c.434A>G (NP_002991.2:p.(Asn145Ser)); therefore the governing generic PP3/BP4 path is REVEL only, and the SpliceAI result is not used for this criterion. REVEL is 0.584, below the supplied generic PP3 supporting threshold of >=0.644 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997), so PP3 is not met. BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence: NM_003000.3:c.434A>G produces NP_002991.2:p.(Asn145Ser), a missense substitution; the applicable generic computational path is REVEL only.
• Local REVEL lookup reports a score of 0.584 for NC_000001.11:g.17027855T>C / NM_003000.3:c.434A>G.
• Generic ClinGen SVI REVEL calibration: PP3 supporting requires >=0.644, as supplied in the case rules; threshold publication is Pejaver et al. 2022, PMID:36413997.
• SpliceAI max delta 0.032 and BayesDel -0.00921904 were not counted for PP3: SpliceAI is the path for intronic, synonymous, or splice-region variants, and BayesDel has no generic ACMG-strength calibration.

Sources

Reasoning

PP5 requires a reputable source to recently report the exact variant as pathogenic when the underlying evidence is unavailable for independent evaluation. The exact ClinVar record for NM_003000.3:c.434A>G (p.Asn145Ser) contains two clinical-laboratory submissions, both classified as Uncertain significance, with zero expert-panel submissions and zero usable criterion-lead submissions. The literature packet and paper extracts contain no exact-variant pathogenic report. Therefore the qualifying PP5 condition is not met.

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_submission_audit.json, exact variant NM_003000.3(SDHB):c.434A>G (p.Asn145Ser): two submissions, both Uncertain significance; expert_panel_submissions=0 and usable_for_criterion_leads=0.
• literature_pass.json: no ai_classified_papers; reviewed exact-variant candidate papers do not report this variant as pathogenic.
• Ordinary laboratory submissions and the aggregate ClinVar label were not treated as PP5 evidence.

Sources

Reasoning

The variant is a missense substitution, NM_003000.3:c.434A>G (NP_002991.2:p.(Asn145Ser)); therefore the governing generic PP3/BP4 path is REVEL only, and the SpliceAI result is not used for this criterion. REVEL is 0.584, above the supplied generic BP4 supporting threshold of <=0.29 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997), so BP4 is not met. The REVEL result is not in the BP4 range; it is not permissible to substitute the low SpliceAI score. BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence: NM_003000.3:c.434A>G produces NP_002991.2:p.(Asn145Ser), a missense substitution; the applicable generic computational path is REVEL only.
• Local REVEL lookup reports a score of 0.584 for NC_000001.11:g.17027855T>C / NM_003000.3:c.434A>G.
• Generic ClinGen SVI REVEL calibration: BP4 supporting requires <=0.29, as supplied in the case rules; threshold publication is Pejaver et al. 2022, PMID:36413997.
• SpliceAI max delta 0.032 was not counted for BP4 because SpliceAI is not the applicable path for a missense variant; BayesDel -0.00921904 was not used because no generic ACMG-strength calibration is established.

Sources

Reasoning

BP6 requires a reputable source to recently report the exact variant as benign when the underlying evidence is unavailable for independent evaluation. The exact ClinVar record for NM_003000.3:c.434A>G (p.Asn145Ser) contains two clinical-laboratory submissions, both classified as Uncertain significance, with zero expert-panel submissions and no benign or likely-benign expert-panel assertion. The reviewed literature contains no exact-variant benign report. Therefore the qualifying BP6 condition is not met.

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_submission_audit.json, exact variant NM_003000.3(SDHB):c.434A>G (p.Asn145Ser): two submissions, both Uncertain significance; expert_panel_submissions=0 and usable_for_criterion_leads=0.
• No reputable exact-variant source in the supplied literature reports a benign or likely-benign classification.
• Ordinary laboratory submissions and the aggregate ClinVar label were not treated as BP6 evidence.

Sources

Reasoning

The variant is NM_003000.3:c.434A>G, p.Asn145Ser, and the available ClinVar record is an uncertain-significance record with no validated criterion-lead submissions or established pathogenic same-amino-acid comparator. The reviewed literature extracts do not mention this variant or an alternate nucleotide change producing p.Asn145Ser. SpliceAI reports a maximum delta score of 0.032, but this does not establish PS1. A verified prior pathogenic p.Asn145Ser variant is required to assess PS1.

Rule

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

Evidence considered

• ClinVar variation 2934131, exact variant NM_003000.3(SDHB):c.434A>G (p.Asn145Ser): classification Uncertain significance; two submissions; zero usable criterion-lead submissions.
• SpliceAI Lookup for NM_003000.3:c.434A>G: maximum delta score 0.032, providing no evidence that the observed result should be treated as a splice-level rather than protein-level comparison.

Still missing

• A validated pathogenic comparator causing p.Asn145Ser by a different nucleotide change is needed.

Sources

Reasoning

No individual-level evidence establishes that NM_003000.3:c.434A>G is de novo in a patient with the disease, confirms both maternity and paternity, or documents absence of a family history. The available records do not provide parental genotypes or the proband's relevant phenotype.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. ... Confirmation of paternity only is insufficient.

Still missing

• Documented disease phenotype in the proband
• Parental testing showing absence of the variant in both biological parents
• Confirmed maternity and paternity
• Documented absence of relevant family history

Reasoning

No variant-specific in vitro or in vivo functional study was identified for SDHB c.434A>G (p.Asn145Ser). The reviewed literature consisted of general clinical or policy sources and did not provide a validated assay, appropriate controls, reproducible functional result, or evidence linking this specific variant to a damaging effect on the gene product. Therefore, the PS3 evidence requirement cannot be assessed.

Rule

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

Evidence considered

• The available variant-specific materials contain no functional assay result for SDHB c.434A>G (p.Asn145Ser).
• The reviewed papers provide general disease or policy information and no variant-specific functional assay, control data, or reproducible damaging-effect measurement.

Still missing

• A variant-specific in vitro or in vivo functional study with appropriate controls and a reproducible damaging result is needed.

Sources

Reasoning

Generic ACMG/AMP PS4 requires a significantly increased prevalence in affected individuals compared with controls; the supplied note specifies that an odds ratio or relative risk must be >5.0 with a confidence interval not including 1.0. The literature_pass.json packet has no ai_classified_papers, and the four PS4-triaged papers were checked against available abstract/full-text material: PMID:20065170 and PMID:26324357 are general ASCO policy statements without SDHB or this variant; PMID:20664475 is a narrative clinical review that does not mention c.434A>G or p.(Asn145Ser); PMID:20301715 has no fetched full text or variant-specific extract. No affected-case/control counts, case frequency with a matched-ancestry control frequency, OR/RR, or 95% CI are available, so no numeric comparison can be performed and PS4 cannot be adjudicated.

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

• literature_pass.json criteria_index lists PMID:20065170, PMID:20301715, PMID:20664475, and PMID:26324357 as PS4 candidates.
• paper_extracts.json: PMID:20065170 and PMID:26324357 do not mention SDHB or the exact variant; PMID:20664475 describes SDHB-associated disease generally but no exact variant, cohort comparison, or case/control counts.
• No available source reports an affected-case frequency, unaffected/population control frequency, OR/RR, or 95% CI for NM_003000.3:c.434A>G.

Still missing

• Variant-specific case and control counts or matched-ancestry case/control frequencies
• Odds ratio or relative risk and 95% confidence interval

Sources

Reasoning

The SDHB VCEP record is present but has no released criteria, and vcep_materials.json has no SDHB domain-table entry. The available evidence reports no statistically significant hotspot for SDHB N145 and no COSMIC finding for this variant. No authoritative evidence establishes residue 145 as a critical, well-established functional domain or hotspot without benign variation. PM1 therefore cannot be assessed 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

• ClinGen SDHB specification, version 1.0, document 101200173: criteria_spec_found is false and no criterion-specific PM1 region is released.
• vcep_materials.json: domain_tables is empty for SDHB.
• Cancer Hotspots query SDHB N145: no statistically significant hotspot row found.
• COSMIC search for SDHB c.434A>G: no result found.

Still missing

• An authoritative SDHB functional-domain or qualifying hotspot source, including evidence of absent benign variation, is needed.

Sources

Reasoning

The target variant is p.Asn145Ser. The supplied PM5 candidate summary contains zero candidates and zero same-residue candidates, and the literature extracts do not identify a pathogenic alternate missense change at residue 145. The available ClinVar record is uncertain significance rather than a validated pathogenic comparator. PM5 cannot be assessed without a confirmed pathogenic different missense change at Asn145.

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 comparator candidate collection: total candidates seen 0 and same-residue candidates 0; the artifact explicitly does not establish a PM5 comparator.
• ClinVar variation 2934131: the target p.Asn145Ser is classified Uncertain significance, with no expert-panel or criterion-lead submission establishing a pathogenic same-residue comparator.

Still missing

• A validated pathogenic missense comparator at residue Asn145 is needed.

Sources

Reasoning

No evidence documents an assumed de novo occurrence of NM_003000.3:c.434A>G. Neither parental genotypes nor a clinical record supporting a de novo interpretation without maternity and paternity confirmation is available.

Rule

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

Still missing

• Evidence that the variant is absent from tested parent or parents
• Clinical documentation supporting a de novo occurrence
• Clarification of whether maternity and paternity were confirmed

Reasoning

No affected relatives, variant genotypes, phenotype concordance, or informative meioses are documented. Therefore, co-segregation with disease in multiple affected family members cannot be evaluated.

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.

Still missing

• Affected family members and their clinical diagnoses
• Variant testing results for affected relatives
• Informative meioses and family structure
• Phenotype consistency across relatives

Reasoning

The supplied evidence does not establish both PP2 requirements for SDHB: a low rate of benign missense variation and missense variants as a common disease mechanism. The single gnomAD v4.1 observation for this variant (allele frequency 6.24608e-07) is variant-level population evidence and cannot establish gene-wide benign missense constraint or the relative disease mechanism. The reviewed SDHB literature describes disease association but does not provide the required gene-wide missense-mechanism analysis.

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 variant record: NM_003000.3:c.434A>G is present at AF 6.24608e-07, 1/1,601,004 alleles, with zero homozygotes; this is not a gene-wide missense constraint metric.
• Li et al. 2010, PMID:20664475, narrative review section 'Pheochromocytoma and paraganglioma, Pathology and molecular genetics': describes SDHB among genes causing familial paraganglioma/pheochromocytoma but does not establish PP2's gene-wide missense requirements.

Still missing

• Gene-wide evidence for low benign missense variation is needed.
• Gene-wide evidence that missense variants are a common SDHB disease mechanism is needed.

Sources

Reasoning

PP4 requires a patient's phenotype or family history that is highly specific for a disease with a single genetic etiology. The available case evidence identifies SDHB and hereditary pheochromocytoma-paraganglioma as the disease context but does not provide the patient's phenotype, family history, or a sufficiently specific clinical presentation. General SDHB disease descriptions in PMID:20664475 cannot substitute for patient-specific phenotype evidence.

Rule

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

Evidence considered

• case_summary.json identifies hereditary pheochromocytoma-paraganglioma as the disease context but does not provide patient-specific phenotype or family-history details.
• PMID:20664475, paper_extracts.json: general SDHB-associated pheochromocytoma/paraganglioma background only; no phenotype for this patient.

Still missing

• Patient phenotype and clinical diagnostic details
• Patient family history and evidence of phenotype specificity

Sources

Reasoning

The variant is present in gnomAD v4.1 at total AF 6.246080584433268e-07 (1/1601004 alleles; homozygotes 0), and the highest observed subpopulation point estimate is 1.6104096882246844e-05 (1/62096 alleles). However, the required filtering metric, grpmax FAF, is not reported, so the specified FAF-based BA1 decision cannot be formally made. The available observed frequencies are far below the generic 0.05 threshold, but BA1 is stand-alone and requires the prescribed filtering-frequency evidence.

Rule

BA1: allele frequency above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium; generic case threshold >=0.05.

Evidence considered

• gnomAD v4.1: total AF=6.246080584433268e-07, 1/1601004 alleles, homozygotes=0.
• gnomAD v4.1: highest observed subpopulation was Remaining individuals, point AF=1.6104096882246844e-05, 1/62096 alleles, homozygotes=0; this point estimate was not used as the BA1 filtering metric.
• Generic BA1 default supplied for this case: >=0.05, described as an ACMG/AMP 2015 stand-alone benign allele-frequency threshold (PMID:25741868).

Still missing

• gnomAD filtering grpmax FAF is unavailable for this variant.
• No governing non-cancer or exome-only population specification was released for SDHB in this case.

Sources

Reasoning

The available gnomAD v4.1 total AF is 6.246080584433268e-07 with one observed allele and no homozygotes, but grpmax FAF is unavailable. In addition, no disorder-specific prevalence, penetrance, allelic heterogeneity, or maximum-credible-allele-frequency inputs are supplied for hereditary SDHB pheochromocytoma-paraganglioma. Therefore, the generic 1% default cannot be responsibly applied or rejected as a disorder-specific BS1 threshold.

Rule

BS1: allele frequency is greater than expected for the disorder; generic default >=0.01 only when appropriate.

Evidence considered

• gnomAD v4.1: total AF=6.246080584433268e-07, 1/1601004 alleles, homozygotes=0; grpmax FAF was null.
• The generic BS1 default supplied for this case is >=0.01, but the governing guidance requires consideration of disorder prevalence, penetrance, allelic heterogeneity, and maximum credible allele frequency before using a default; Whiffin et al. 2017, PMID:28518168.
• The case provides no validated SDHB-specific prevalence, penetrance, allelic-heterogeneity, or maximum-credible-frequency inputs for this variant or disorder.

Still missing

• gnomAD filtering grpmax FAF is unavailable for this variant.
• No disorder-specific maximum credible allele-frequency calculation inputs are available.

Sources

Reasoning

gnomAD v4.1 reports no homozygotes for the variant, but this absence does not establish that the variant was observed in a healthy adult. The available population record does not provide individual age, phenotype, ascertainment, or validated healthy-adult status, and no qualifying healthy-adult observation is documented elsewhere in the supplied evidence.

Rule

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 aggregate record: 1 observed allele in 1601004 total alleles and homozygotes=0; the record contains no individual-level age or phenotype information.
• The supplied case framework identifies hereditary SDHB pheochromocytoma-paraganglioma as autosomal dominant, but no healthy-adult observation for this variant is reported.

Still missing

• No qualifying healthy-adult carrier observation with age and phenotype information is documented.
• gnomAD aggregate data do not establish healthy-adult status for individual carriers.

Sources

Reasoning

No variant-specific in vitro or in vivo functional study was identified for SDHB c.434A>G (p.Asn145Ser). The reviewed literature consisted of general clinical or policy sources and did not provide a validated assay, appropriate controls, reproducible functional result, or evidence showing no damaging effect on protein function or splicing. Therefore, the BS3 evidence requirement cannot be assessed.

Rule

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

Evidence considered

• The available variant-specific materials contain no functional assay result for SDHB c.434A>G (p.Asn145Ser).
• The reviewed papers provide general disease or policy information and no variant-specific functional assay, control data, or reproducible benign-effect measurement.

Still missing

• A variant-specific in vitro or in vivo functional study with appropriate controls and a reproducible result showing no damaging effect on protein function or splicing is needed.

Sources

Reasoning

No affected family members with documented variant-negative results are identified, and no family structure or phenotype information is available to evaluate non-segregation. The possibility of phenocopies or more than one pathogenic variant therefore cannot be assessed.

Rule

Lack of segregation in affected members of a family.

Still missing

• Affected relatives tested for the variant
• Reliable clinical diagnoses and phenotype details for relatives
• Family structure and informative inheritance observations
• Assessment of phenocopies or additional pathogenic variants

Reasoning

The evidence supports SDHB loss of function as a disease mechanism, but it does not establish that primarily truncating variants are known to cause disease. The reviewed SDHB narrative review provides gene-level disease context without a variant-spectrum analysis showing predominance of truncating variants over missense variants. Therefore BP1 cannot be assessed from the supplied evidence.

Rule

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

Evidence considered

• Li et al. 2010, PMID:20664475, narrative review section 'Pheochromocytoma and paraganglioma, Pathology and molecular genetics': identifies germline SDHB mutations in familial disease but does not establish a primarily truncating variant spectrum.
• Case gene-level context: SDHB loss of function is supported, but the supplied evidence does not quantify or classify the pathogenic variant spectrum as primarily truncating.

Still missing

• A validated SDHB disease-variant spectrum demonstrating that primarily truncating variants cause disease is needed.

Sources

Reasoning

BP2 requires an observed trans relationship with a pathogenic variant for a fully penetrant dominant disorder, or an observed cis relationship with a pathogenic variant in any inheritance pattern. The case evidence identifies NM_003000.3:c.434A>G (p.Asn145Ser) but provides no parental or offspring testing, phase determination, affected-proband observation, or documented pathogenic variant in cis or trans. ClinVar contains two germline submissions classified as uncertain significance, without a phase or allelic observation for this variant. The criterion therefore cannot be assessed from the available evidence.

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

• ClinVar variation 2934131 contains two germline submissions for NM_003000.3:c.434A>G (p.Asn145Ser), both classified as uncertain significance, with no reported cis/trans phase observation.
• The SDHB disease context in the CSPEC record is autosomal dominant, so the BP2 trans pathway would require a documented pathogenic partner and phase determination; neither is provided.

Still missing

• Documented phase testing in an affected proband or family showing NM_003000.3:c.434A>G in trans or cis with a pathogenic variant.
• A validated pathogenic or likely pathogenic classification for the partner variant.

Sources

Reasoning

BP5 requires the variant to be found in a case with an alternate molecular basis for disease. The supplied evidence contains no case report or molecular finding establishing an alternate molecular diagnosis for a patient carrying NM_003000.3:c.434A>G. General disease reviews and the uncertain-significance ClinVar submissions do not establish this criterion.

Rule

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

Evidence considered

• No case-specific alternate molecular diagnosis is reported in the supplied evidence.
• The ClinVar record contains only two uncertain-significance clinical-laboratory submissions and does not document BP5 evidence.

Still missing

• A case report documenting the variant in a patient with an independently established alternate molecular cause