Starting
Initialising…
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EZH2
Final classification
Likely Benign
EZH2 c.1852-9A>C · p.?
EZH2

NM_004456.4:c.1852-9A>C is an intronic variant in EZH2 located 9 bases upstream of exon 15, outside canonical splice consensus sites.

Gene
EZH2
Transcript
NM_004456.4
HGVS · transcript:coding
NM_004456.4:c.1852-9A>C
Consequence
N/A
GRCh38
chr7:148811729 T>G
GRCh37
chr7:148508821 T>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, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
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, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP4BP6 Likely Benign
EZH2 c.1852-9A>C

NM_004456.4:c.1852-9A>C is an intronic variant in EZH2 located 9 bases upstream of exon 15, outside canonical splice consensus sites.1 This variant is present in gnomAD at very low frequency (v2.1: 11/246,568 alleles, AF=0.0045%; v4.1: 73/1,608,258 alleles, AF=0.0045%) with no homozygotes observed. The allele frequency falls well below the 0.1% PM2 threshold (PM2_supporting).2 SpliceAI predicts no significant splice impact (max delta score = 0.02), providing computational evidence that the variant does not disrupt normal splicing (BP4_supporting).3 ClinVar classifies this variant as Likely benign (VariationID 416828) based on a submission from Labcorp Genetics with ACMG criteria provided. This constitutes supporting benign evidence from a reputable clinical source (BP6_supporting).4 PVS1 is not applicable as the variant lies outside canonical splice ±1,2 consensus sites and does not fall into null-variant buckets per ClinGen SVI recommendations (PMC6185798). PM5, PP2, BP1, BP7 are not applicable as the variant is intronic, not missense or synonymous. BP3, PM3, PM4 were skipped per instruction as trivially not applicable.5 Applying generic ACMG/AMP 2015 final classification combination rules: two supporting benign criteria (BP4, BP6) are met, which reaches the threshold for Likely benign. One supporting pathogenic criterion (PM2) is also met but does not alter the Likely benign classification under the standard combination rules.6

PM2 + BP4 + BP6 Likely Benign
Gene diagram · NM_004456.4 · variants mapped to exon structure
EZH2 NM_004456.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.53907e-05; MAF= 0.00454%, 73/1608258 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.94113e-05; MAF= 0.00594%, 70/1178228 alleles, homozygotes = 0); grpmax FAF= 4.788e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.46124e-05; MAF= 0.00446%, 11/246568 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.74003e-05; MAF= 0.00974%, 11/112936 alleles, homozygotes = 0); grpmax FAF= 5.414e-05.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0045% · 73 / 1,608,258
      0 hom · FAF 0.0048%
      European (non-Finnish)
      70 / 1,178,228
      0.0059%
      Remaining individuals
      2 / 62,414
      0.0032%
      South Asian
      1 / 91,016
      0.0011%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0045% · 11 / 246,568
      0 hom · FAF 0.0054%
      European (non-Finnish)
      11 / 112,936
      0.0097%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 416828)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 2 PMIDs not cited in assessment
      23865096 ↗ EZH2-Related Overgrowth. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR