SDHB c.73-29del, p.?

Reasoning

The SDHB CSPEC identifies NM_003000.2 as the preferred transcript but provides no criterion-level PVS1 rule; generic ACMG/AMP/ClinGen SVI PVS1 assessment therefore applies. NM_003000.3:c.73-29del is a one-base intronic deletion 29 bases upstream of coding position c.73, not a nonsense, frameshift, or canonical splice (±1/2) variant. The predicted protein consequence is p.?, and SpliceAI shows no predicted splice effect (maximum delta 0.002). There is no RNA, minigene, or protein evidence demonstrating aberrant splicing, NMD, or loss of SDHB protein. It does not meet a PVS1 null-variant or splice-disruption bucket.

Rule

Generic ACMG/AMP PVS1, informed by ClinGen SVI PVS1 recommendations: apply only to a variant predicted to cause loss of function in a gene where loss of function is an established disease mechanism, including nonsense, frameshift, canonical ±1/2 splice variants, or a non-canonical splice variant with demonstrated null splicing consequence. This intronic c.73-29 deletion has neither a qualifying variant class nor demonstrated splice/NMD consequence.

Evidence considered

• The SDHB Endocrine Tumor Predisposition CSPEC v1.0 lists NM_003000.2 as the preferred transcript but contains no extracted criterion-level PVS1 rule, so no gene-specific PVS1 strength modification is available.
• Variant normalization identifies NM_003000.3:c.73-29del as intronic (VariantValidator exon annotation 1i) with predicted protein consequence NP_002991.2:p.?.
• The generic PVS1 assessment places the variant in bucket 'other', with canonical splice consensus false and no application of the generic PVS1 null-variant framework.
• SpliceAI returns DS_AG 0.000, DS_AL 0.000, DS_DG 0.002, and DS_DL 0.001 (maximum delta 0.002), providing no predicted splice-disruption signal.
• PMID:25741868 states that splice-site variants require RNA- or protein-based functional analysis to confirm their impact; no such assay is present for this allele.

Still missing

• No constitutional RNA study (ideally with NMD inhibition) or validated minigene assay is available to directly exclude or demonstrate a cryptic splicing effect of this non-canonical intronic deletion.

Sources

Reasoning

PM2 is not met because the variant is observed repeatedly in population databases rather than being absent from controls. gnomAD v4.1 reports 1253 alternate alleles and two homozygotes, gnomAD v2.1 reports 101 alternate alleles, and gnomAD-Canada reports eight alternate alleles.

Rule

Generic ACMG/AMP PM2 requires absence or near-absence of the variant from appropriate population databases; this variant is present in gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada.

Evidence considered

• gnomAD v4.1 contains the variant at 1253/1593262 alleles with two homozygotes.
• gnomAD v2.1 contains the variant at 101/258314 alleles with no homozygotes.
• gnomAD-Canada v1.0 contains the variant at 8/18420 alleles with no homozygotes.
• Because the variant is present in multiple reference-population datasets, the generic PM2 absence-from-controls requirement is not satisfied.

Sources

Reasoning

No criterion-level PM4 instruction is available in the SDHB CSPEC, so generic ACMG/AMP PM4 applies. This is an intronic one-base deletion with protein prediction p.?; it is not an in-frame coding indel, does not establish any protein-length change, and is not a stop-loss variant. PM4 is not met.

Rule

Generic ACMG/AMP PM4: protein length changes resulting from in-frame insertions/deletions in a non-repeat region or stop-loss variants. The intronic allele has no predicted protein-length change.

Evidence considered

• The SDHB CSPEC provides no extracted criterion-level PM4 specification.
• Variant normalization places c.73-29del in intronic sequence and gives NP_002991.2:p.? rather than an in-frame amino-acid deletion/insertion or stop-loss consequence.
• SpliceAI maximum delta is 0.002, so there is no prediction of splice alteration that would support an inferred protein-length change.
• PMID:25741868 supplies the generic ACMG/AMP framework under which PM4 concerns protein-length changes from in-frame indels in non-repeat regions or stop-loss variants.

Still missing

• No RNA assay is available to determine whether this intronic allele has an unexpected transcript consequence; current splice prediction provides no indication of a protein-length-changing effect.

Sources

Reasoning

The available SpliceAI result does not support a splice-altering effect: its maximum delta score is 0.002. This intronic deletion is not a missense variant, and no missense-predictor result is applicable.

Rule

SDHB ClinGen Endocrine Tumor Predisposition Expert Panel framework has no applicable PP3 rule in the supplied materials; generic ACMG/AMP computational evidence was considered. The observed splice prediction is not pathogenic-supporting.

Evidence considered

• SpliceAI Lookup for NM_003000.3:c.73-29del reports DS_AG 0.000, DS_AL 0.000, DS_DG 0.002, DS_DL 0.001, and maximum delta score 0.002; it summarizes the prediction as no significant splice impact.
• The SDHB ClinGen Endocrine Tumor Predisposition Expert Panel framework was reviewed first. The supplied framework contains no PP3-specific rule or pre-assigned lookup result for this variant.

Sources

Reasoning

ClinVar has no exact-variant expert-panel pathogenic or likely pathogenic assertion for NM_003000.3(SDHB):c.73-29del.

Rule

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

Evidence considered

• ClinVar variation 998298 is an exact transcript-HGVS match, but its expert_panels field is empty and the submission audit reports zero expert-panel submissions.
• The available ClinVar submissions are ordinary single-submitter classifications (Likely benign, Benign, and Uncertain significance), none of which may trigger PP5.

Still missing

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

Sources

Reasoning

The variant does not meet a stand-alone benign frequency threshold. gnomAD v4.1 reports AF 0.000786437 overall and maximum population AF 0.000975387 in European non-Finnish individuals; gnomAD v2.1 reports AF 0.000390997 overall and maximum population AF 0.000635949; gnomAD-Canada reports AF 0.000434311. These frequencies are below the generic BA1 threshold of 1% used for this non-structured CSPEC fallback assessment.

Rule

Generic ACMG/AMP BA1 stand-alone benign frequency threshold: population allele frequency greater than 1%; no applicable structured SDHB-specific threshold was available in the CSPEC extraction.

Evidence considered

• The applicable SDHB ClinGen specification is present, but its extracted ruleset is unstructured and contains no criterion-specific population thresholds; therefore generic ACMG/AMP population assessment was used as fallback.
• gnomAD v4.1: 1253/1593262 alleles, AF 0.000786437 overall; European non-Finnish maximum observed AF 0.000975387 (1138/1166716 alleles).
• gnomAD v2.1: 101/258314 alleles, AF 0.000390997 overall; European non-Finnish maximum observed AF 0.000635949 (75/117934 alleles).
• gnomAD-Canada v1.0: 8/18420 alleles, AF 0.000434310532, with no homozygotes.
• All observed frequencies are below 0.01 (1%), so BA1 is not met.

Sources

Reasoning

The observed population frequency is below the benign-supporting BS1 threshold used for this assessment. The highest reported frequency is 0.000975387 in gnomAD v4.1 European non-Finnish individuals, with gnomAD v4.1 maximum group FAF 0.00092765; gnomAD v2.1 maximum group FAF is 0.00052322 and gnomAD-Canada AF is 0.000434311. None exceeds 0.3%.

Rule

Generic population-frequency BS1 threshold used for this assessment: allele frequency greater than 0.3%; no applicable structured SDHB-specific threshold was available in the CSPEC extraction.

Evidence considered

• The applicable SDHB ClinGen specification is present, but its extracted ruleset is unstructured and contains no criterion-specific population thresholds; generic ACMG/AMP population assessment was therefore used as fallback.
• gnomAD v4.1 maximum observed population AF was 0.000975387 in European non-Finnish individuals; maximum group FAF was 0.00092765.
• gnomAD v2.1 maximum observed population AF was 0.000635949 in European non-Finnish individuals; maximum group FAF was 0.00052322.
• gnomAD-Canada v1.0 AF was 0.000434310532.
• The maximum observed frequency is below 0.003 (0.3%), so BS1 is not met.

Sources

Reasoning

No criterion-level BP3 instruction is available in the SDHB CSPEC, so generic ACMG/AMP BP3 applies. BP3 requires an in-frame coding insertion/deletion in a repetitive region without known function. c.73-29del is intronic, has no established in-frame protein consequence, and the available record does not identify a qualifying coding repeat-region indel. BP3 is not met.

Rule

Generic ACMG/AMP BP3: in-frame insertions/deletions in a repetitive region without a known function. This non-canonical intronic deletion is not an in-frame coding indel, irrespective of local low-complexity annotation.

Evidence considered

• The SDHB CSPEC provides no extracted criterion-level BP3 specification.
• Variant normalization identifies a one-base intronic deletion at c.73-29 with protein consequence p.?, not an in-frame coding indel.
• SpliceAI maximum delta is 0.002, providing no predicted splice effect that would create a coding length change.
• PMID:25741868 supplies the generic ACMG/AMP BP3 framework for in-frame indels in repetitive regions without known function.

Still missing

• No direct transcript assay is available, but the absence of a predicted splice effect means there is currently no basis to posit an in-frame coding indel for BP3 evaluation.

Sources

Reasoning

ClinVar has no exact-variant expert-panel benign or likely benign assertion for NM_003000.3(SDHB):c.73-29del.

Rule

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

Evidence considered

• ClinVar variation 998298 is an exact transcript-HGVS match, but its expert_panels field is empty and the submission audit reports zero expert-panel submissions.
• The available ClinVar Benign and Likely benign entries are ordinary single-submitter laboratory assertions and must not trigger BP6.

Still missing

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

Sources

Reasoning

No auditable case-level evidence establishes that NM_003000.3:c.73-29del is absent from both biological parents or that it arose de novo in an affected proband. The case bundle contains no proband pedigree, parental genotype results, parentage information, or phenotype documentation. ClinVar includes one submission annotated with origin as maternal, but provides no supporting parental test report and is insufficient to adjudicate PS2. The applicable SDHB ClinGen specification was identified, but its retrieved rule payload is empty and incomplete; no usable gene-specific PS2 rule was available.

Evidence considered

• The retrieved SDHB ClinGen specification is applicable to hereditary pheochromocytoma-paraganglioma but contains no populated criterion rules or usable PS2 rule payload.
• The case bundle provides no proband or parental segregation/de novo testing data.
• ClinVar records one single-submitter entry with origin annotated as maternal, without an auditable parental-genotype report or criterion-level evidence; this cannot establish or exclude PS2.
• The variant is an intronic deletion with predicted protein consequence p.?; no segregation inference was made from variant consequence or from any source classification.

Still missing

• Affected-proband phenotype and clinical indication
• Validated variant testing results for both biological parents
• Parentage confirmation and details of the de novo assessment
• Usable SDHB-specific PS2 rule text from the applicable specification

Sources

Reasoning

No validated, variant-specific functional assay evidence was identified for NM_003000.3:c.73-29del. The available literature extraction contains no assay, RNA result, protein result, cellular phenotype, assay controls, or quantitative calibration for this variant. The SDHB ClinGen specification is present, but its retrieved ruleset is incomplete and provides no usable PS3 strength rule; therefore generic ACMG/AMP functional-study requirements apply. A splice-region prediction or a general statement that functional testing is needed cannot establish PS3.

Evidence considered

• The governing source is the ClinGen Endocrine Tumor Predisposition Specification for SDHB, version 1.0 (source key cspec). The retrieved specification is marked incomplete and contains no usable PS3 rule payload.
• The case evidence bundle and paper extraction for PMID:25741868 contain no SDHB-specific or c.73-29del-specific functional result. The paper states: 'For splice site variants, the variant may lead to exon skipping, shortening or inclusion of intronic material, due to alternative donor/acceptor site usage or creation of new sites. Although splice site variants are predicted to lead to a null effect, confirmation of impact requires functional analysis by either RNA or protein analysis.'

Still missing

• Variant-specific RNA or protein assay demonstrating an abnormal effect is absent.
• No validated assay methodology, appropriate positive/negative controls, or quantitative result is available.
• No evidence establishes that an available assay measures a biologically relevant SDHB function for this variant.
• No evidence supports calibration to supporting, moderate, or strong PS3 strength.

Sources

Reasoning

No exact-variant case-control or statistically supported enrichment evidence was identified for SDHB c.73-29del.

Rule

SDHB VCEP framework applies; because its supplied ruleset has no structured PS4 specification, generic ACMG/AMP requires a statistically increased prevalence of the exact variant in affected individuals compared with controls.

Evidence considered

• The applicable SDHB Endocrine Tumor Predisposition specification was identified, but the supplied ruleset contains no structured PS4 rule or threshold.
• The literature bundle's PS4 candidates are general clinical-policy papers; their precomputed extracts state that c.73-29del is not mentioned, so they provide no case or control counts for this variant.

Still missing

• An ascertainment-defined case cohort with exact-variant counts and an ancestry-matched control comparison is needed to assess enrichment.

Sources

Reasoning

No auditable case-level evidence describes NM_003000.3:c.73-29del as presumed de novo when parental testing was incomplete or unavailable. The bundle lacks a proband report, parental testing status, parentage information, and phenotype details. A ClinVar maternal-origin annotation is not evidence of presumed de novo occurrence and does not provide sufficient case documentation for PM6. The applicable SDHB specification was retrieved, but no usable gene-specific PM6 rule was available.

Evidence considered

• The retrieved SDHB ClinGen specification has an empty, incomplete rule payload and provides no usable PM6-specific instruction.
• No case-level publication, pedigree, parental testing result, or clinical report in the bundle documents presumed de novo occurrence.
• ClinVar contains a maternal-origin annotation for one single-submitter record, but no documentation that would support PM6.

Still missing

• Case report identifying the proband and phenotype
• Documentation that parental testing was incomplete or unavailable
• Evidence supporting presumed de novo status and parentage
• Usable SDHB-specific PM6 rule text from the applicable specification

Sources

Reasoning

No affected or unaffected relatives, informative meioses, family structure, genotype results, or phenotype-segregation data are provided for NM_003000.3:c.73-29del. Therefore, neither cosegregation nor a PP1 strength can be assessed. The retrieved SDHB ClinGen specification is applicable but incomplete and contains no usable PP1 rule payload.

Evidence considered

• The case bundle contains no family pedigree, relative genotypes, phenotype assessments, or informative meioses.
• The applicable SDHB ClinGen specification was found, but its retrieved rule payload is empty and incomplete, so no gene-specific PP1 threshold can be applied.
• No paper extract in the bundle reports variant-specific family segregation for c.73-29del.

Still missing

• Pedigree with affected and unaffected relatives
• Variant genotypes for informative relatives
• Phenotype status and diagnostic criteria for each relative
• Number of informative meioses and segregation analysis
• Usable SDHB-specific PP1 rule and strength thresholds

Sources

Reasoning

No phenotype for the proband or exact-variant carrier is provided, so phenotype specificity for hereditary pheochromocytoma-paraganglioma cannot be assessed.

Rule

SDHB VCEP framework applies; because no structured PP4 specification is supplied, generic ACMG/AMP PP4 requires a highly specific phenotype in a variant carrier.

Evidence considered

• The SDHB VCEP material identifies hereditary pheochromocytoma-paraganglioma as the relevant autosomal-dominant disease, but supplies no structured PP4 rule.
• No case-level phenotype data or exact-variant clinical report is present in the consolidated evidence bundle.

Still missing

• Provide the individual's clinical phenotype, tumor type(s), age at diagnosis, biochemical findings, and exclusion of relevant alternative etiologies.

Sources

Reasoning

gnomAD v4.1 reports two homozygotes overall, including one in the European non-Finnish population and one in the South Asian population. However, gnomAD aggregate data do not establish that these individuals are healthy adults, unaffected with respect to SDHB-related disease, appropriately phenotyped, or free of ascertainment and age-related penetrance artifacts. The available evidence therefore cannot establish BS2.

Rule

Generic ACMG/AMP BS2 requires observation of the variant in healthy adults, typically in the homozygous state for a dominant condition; aggregate gnomAD homozygote counts without individual phenotype and age data are insufficient.

Evidence considered

• gnomAD v4.1 reports total homozygotes = 2; one homozygote is reported in European non-Finnish individuals and one in South Asian individuals.
• A population database homozygote count alone does not demonstrate the BS2 requirement of observation in healthy adults because individual phenotype, age, ascertainment, and penetrance information are not provided.

Still missing

• Individual-level phenotype and health-status data for the two gnomAD v4.1 homozygotes are unavailable.
• Age and clinical ascertainment information sufficient to assess SDHB-related disease penetrance in the homozygotes is unavailable.
• No independent report confirms unaffected adult homozygotes for this exact variant.

Sources

Reasoning

No validated, variant-specific functional study demonstrating preserved SDHB function was identified for NM_003000.3:c.73-29del. The available literature extraction contains no benign functional assay result, assay controls, biological relevance assessment, or quantitative calibration. The SDHB ClinGen specification is present but incomplete and provides no usable BS3 strength rule; generic ACMG/AMP criteria therefore cannot be applied without a well-established assay showing no damaging effect.

Evidence considered

• The governing source is the ClinGen Endocrine Tumor Predisposition Specification for SDHB, version 1.0 (source key cspec). The retrieved specification is marked incomplete and contains no usable BS3 rule payload.
• The case evidence bundle and paper extraction for PMID:25741868 contain no SDHB-specific or c.73-29del-specific benign functional result. The paper discusses the need for RNA- or protein-based functional analysis of splice-region variants but does not report such an analysis for this variant.

Still missing

• No variant-specific functional assay demonstrating retained function is available.
• No validated assay methodology, appropriate positive/negative controls, or quantitative result is available.
• No evidence establishes that an available assay measures a biologically relevant SDHB function for this variant.
• No evidence supports calibration to supporting, moderate, or strong BS3 strength.

Sources

Reasoning

No unaffected relatives known to carry or not carry NM_003000.3:c.73-29del are described, and no phenotype-confirmed non-segregation analysis is available. Consequently, BS4 cannot be assessed. The retrieved SDHB ClinGen specification is applicable but incomplete and contains no usable BS4 rule payload.

Evidence considered

• The case bundle contains no unaffected relative data, genotype results, pedigree, or non-segregation analysis.
• The applicable SDHB ClinGen specification was retrieved, but its rule payload is empty and incomplete and supplies no usable BS4 instruction.
• No paper extract in the bundle reports variant-specific non-segregation for c.73-29del.

Still missing

• Pedigree and phenotypic status of relatives
• Validated genotypes for unaffected relatives
• Assessment of phenotype specificity and age-related penetrance
• Number of informative non-segregating meioses
• Usable SDHB-specific BS4 rule text

Sources

Reasoning

The applicable SDHB framework specifies autosomal dominant inheritance, so BP2 could be relevant if the variant were documented in cis or trans with a known pathogenic variant in an affected or unaffected individual as appropriate. The case-evidence bundle contains no individual-level genotype, phase, family, or affected-proband observation establishing such an allelic relationship. Therefore BP2 cannot be assessed.

Rule

Assess BP2 only when the variant is observed in trans with a pathogenic variant, or in cis with a pathogenic variant in a relevant dominant-disease context, with adequate individual-level phase and phenotype information; no such evidence is available here.

Evidence considered

• The governing SDHB framework identifies autosomal dominant inheritance.
• The consolidated case-evidence bundle provides no documented affected proband, family segregation, pathogenic-variant co-occurrence, or cis/trans phase result for NM_003000.3:c.73-29del.
• Population observations in gnomAD do not establish the individual-level cis/trans allelic relationship required for BP2.

Still missing

• Individual-level co-occurrence data with a known pathogenic SDHB variant are absent.
• Phase information (cis or trans) is absent.
• Affected status and inheritance details for any alleged co-occurrence are absent.

Sources

Reasoning

SpliceAI predicts no significant splice impact (maximum delta score 0.002), but the supplied evidence contains only this single predictor result and no verified, published calibration threshold for applying BP4 to this result. Therefore BP4 is not assigned.

Rule

No applicable SDHB-specific BP4 specification is supplied. Under generic ACMG/AMP, benign computational evidence requires an applicable calibrated computational basis; the available single SpliceAI result lacks a supplied verified published BP4 calibration threshold.

Evidence considered

• SpliceAI Lookup for NM_003000.3:c.73-29del reports a maximum delta score of 0.002 and summarizes the prediction as no significant splice impact.
• The governing SDHB ClinGen Endocrine Tumor Predisposition Expert Panel framework is present but the supplied rule payload and criteria list contain no PP3/BP4 specification or variant-specific pre-assignment.

Still missing

• A verified published calibration threshold and the required computational-evidence combination rule for BP4 are not supplied for this non-missense intronic deletion.
• No SDHB-specific PP3/BP4 lookup or rule is provided in the governing framework.

Sources

Reasoning

No case-level evidence shows that the relevant phenotype is fully explained by another molecular diagnosis.

Rule

SDHB VCEP framework applies; because no structured BP5 specification is supplied, generic ACMG/AMP BP5 requires a variant in a case whose phenotype is fully explained by another molecular diagnosis.

Evidence considered

• The supplied SDHB VCEP ruleset contains no structured BP5 specification.
• No dual-diagnosis, alternative molecular finding, or case-level phenotype information is present in the consolidated evidence bundle.

Still missing

• Provide the individual's phenotype and comprehensive molecular results demonstrating an alternative diagnosis that fully explains it.

Sources