Starting
Initialising…
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H3C2
Final classification
VUS
H3C2 c.244G>C · p.Asp82His
H3C2

NM_003537.3:c.244G>C (p.Asp82His) is a missense variant in H3C2, a histone H3 gene recurrently altered in pediatric cancers including glioblastoma.

Gene
H3C2
Transcript
NM_003537.3
HGVS · transcript:coding
NM_003537.3:c.244G>C
Consequence
N/A
GRCh38
chr6:26031817 C>G
GRCh37
chr6:26032045 C>G
Basis gene-specific framework 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.
gene-specific framework 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
H3C2 c.244G>C

NM_003537.3:c.244G>C (p.Asp82His) is a missense variant in H3C2, a histone H3 gene recurrently altered in pediatric cancers including glioblastoma.1 The variant is absent from gnomAD v2.1 and v4.1 population databases (PM2_Supporting).2 The variant is not present in COSMIC and does not lie within a statistically significant mutational hotspot. In silico predictions are equivocal: REVEL score is 0.585 and BayesDel is 0.631, both borderline toward pathogenicity, while SpliceAI predicts no splicing impact (max delta 0.08).3 No functional studies, segregation data, de novo reports, or case-control evidence have been identified for this variant. OncoKB reports no variant-specific functional evidence.4 A single ClinVar submission from Invitae classifies the variant as uncertain significance; no expert panel or multi-submitter consensus is available.5 Only one supporting pathogenic criterion (PM2_Supporting) is met. No benign criteria are met. The evidence is insufficient to classify the variant as pathogenic or benign.6

PM2 VUS
3 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_003537.3 · variants mapped to exon structure
H3C2 NM_003537.3
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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.585. BayesDel score = 0.631182.
      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. H3C2, a histone variant, is recurrently altered by mutation in various pediatric cancers, including pediatric glioblastoma.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots