Starting
Initialising…
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SDHA
Final classification
VUS
SDHA c.840C>T · p.Ile280=
SDHA

The SDHA c.840C>T (p.Ile280=) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Likely benign with criteria provided from a single submitter.

Gene
SDHA
Transcript
NM_004168.4
HGVS · transcript:coding
NM_004168.4:c.840C>T
Consequence
N/A
GRCh38
chr5:230945 C>T
GRCh37
chr5:231060 C>T
Basis Generic ACMG/AMP 2015 final-classification combination rules were used as the applicable fallback framework because no official or custom gene-specific final-classification framework was available.
Generic ACMG/AMP 2015 final-classification combination rules were used as the applicable fallback framework because no official or custom gene-specific final-classification framework was available.
Classification rationale
PM2 BP7 VUS
SDHA c.840C>T

The SDHA c.840C>T (p.Ile280=) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Likely benign with criteria provided from a single submitter.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the default PM2 rarity threshold of 0.1% and does not reach the BS1 (>0.3%) or BA1 (>1%) benign frequency thresholds.2 In silico assessment is consistent with a benign synonymous effect, as the variant does not change the amino acid sequence and SpliceAI predicts no significant splice impact with a maximum delta score of 0.04.3

PM2 + BP7 VUS
Gene diagram · NM_004168.4 · variants mapped to exon structure
SDHA NM_004168.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (2 clinical laboratories).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB oncogenicity for this specific variant: Unknown Oncogenic Effect (variant has not been individually curated).
      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.
      Hotspots ↗
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      Cancer hotspots