Starting
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SDHB
Final classification
VUS
SDHB c.172A>G · p.Met58Val
SDHB

NM_003000.3:c.172A>G (p.Met58Val) is a missense variant in SDHB, a tumor suppressor gene associated with autosomal dominant hereditary pheochromocytoma-paraganglioma.

Gene
SDHB
Transcript
NM_003000.3
HGVS · transcript:coding
NM_003000.3:c.172A>G
Consequence
N/A
GRCh38
chr1:17044789 T>C
GRCh37
chr1:17371284 T>C
Basis ClinGen Endocrine Tumor Predisposition Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SDHB Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
ClinGen Endocrine Tumor Predisposition Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SDHB Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
SDHB c.172A>G

NM_003000.3:c.172A>G (p.Met58Val) is a missense variant in SDHB, a tumor suppressor gene associated with autosomal dominant hereditary pheochromocytoma-paraganglioma.1 This variant is absent from gnomAD v2.1 and v4.1, supporting PM2 at supporting level per generic ACMG/AMP 2015 criteria.2 Six clinical laboratories have submitted this variant to ClinVar, all classifying it as Uncertain Significance (ClinVar variation ID: 459138).3 In silico predictions are indeterminate: SpliceAI predicts no splice impact (max delta 0.00) and BayesDel score is 0.338, which does not reach a pathogenic or benign threshold. REVEL score is unavailable.4 No functional studies, case reports, segregation data, or de novo observations have been identified for this variant in the reviewed literature or curated databases.5 No pathogenic missense variant at the same amino acid residue (Met58) was identified for PM5 comparison.6 The ClinGen Endocrine Tumor Predisposition Expert Panel specifications for SDHB (version 1.0.0) were identified but contained no parsed criterion-level rules; classification adheres to generic ACMG/AMP 2015 framework.7 With only PM2_Supporting met and no additional pathogenic or benign criteria satisfied, the variant remains a Variant of Uncertain Significance per ACMG/AMP 2015 combination rules (PMID:25741868).8

PM2 VUS
4 spliceai ↗bayesdel
6 pm5_candidates
7 cspec ↗generic_acmg_combination_rules
8 generic_acmg_combination_rules
Gene diagram · NM_003000.3 · variants mapped to exon structure
SDHB NM_003000.3
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 459138)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.338173.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. SDHB, a subunit of succinate dehydrogenase, is infrequently altered in cancer.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 12 PMIDs not cited in assessment
      20816580 ↗ Endocrine cancer predisposition syndromes: hereditary paraganglioma, multiple endocrine neoplasia type 1, multiple endocrine neoplasia type 2, and hereditary thyroid cancer. CLINVAR
      23852704 ↗ Tumor markers in colorectal cancer, gastric cancer and gastrointestinal stromal cancers: European group on tumor markers 2014 guidelines update. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      20301715 ↗ Hereditary Paraganglioma-Pheochromocytoma Syndromes. CLINVAR
      20664475 ↗ The North American Neuroendocrine Tumor Society consensus guideline for the diagnosis and management of neuroendocrine tumors: pheochromocytoma, paraganglioma, and medullary thyroid cancer. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      24319509 ↗ Canadian guideline on genetic screening for hereditary renal cell cancers. CLINVAR
      22685257 ↗ The UK NEQAS for Molecular Genetics scheme for gastrointestinal stromal tumour: findings and recommendations following four rounds of circulation. CLINVAR
      24893135 ↗ Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
      33939658 ↗ The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma. CLINVAR