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CEBPA
Final classification
VUS
CEBPA c.47_48delinsA · p.Ser16LysfsTer144
CEBPA

PVS1 (Very Strong): NM_004364.3:c.47_48delinsA is a frameshift null variant in CEBPA, a gene where loss-of-function is an established mechanism for autosomal dominant familial AML predisposition. The variant is predicted to produce p.Ser16LysfsTer144, ablating expression of the full-length p42 isoform. Assessed under ClinGen SVI PVS1 framework (PMC6185798).

Gene
CEBPA
Transcript
NM_004364.3
HGVS · transcript:coding
NM_004364.3:c.47_48delinsA
Consequence
N/A
GRCh38
chr19:33302367 GC>T
GRCh37
chr19:33793273 GC>T
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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
CEBPA c.47_48delinsA

PVS1 (Very Strong): NM_004364.3:c.47_48delinsA is a frameshift null variant in CEBPA, a gene where loss-of-function is an established mechanism for autosomal dominant familial AML predisposition. The variant is predicted to produce p.Ser16LysfsTer144, ablating expression of the full-length p42 isoform. Assessed under ClinGen SVI PVS1 framework (PMC6185798).1 PM2 (Supporting): The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, consistent with a rare pathogenic variant.2 Classification: Variant of Uncertain Significance (VUS). Met criteria: PVS1 (Very Strong) + PM2 (Supporting). Under generic ACMG/AMP 2015 final combination rules (PMID:25741868), 1 Very Strong + 1 Supporting does not reach the threshold for Likely Pathogenic (which requires at least 1 Very Strong + 1 Moderate, or 1 Strong + 2 Supporting). While the variant is strongly suggestive of pathogenicity based on its molecular consequence and absence from population databases, additional evidence (functional data, segregation, case observations, or ClinVar classification by an expert panel) would be needed to upgrade to Likely Pathogenic.3

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
3 generic_acmg_combination_rules
Gene diagram · NM_004364.3 · variants mapped to exon structure
CEBPA NM_004364.3
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.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; curated oncogenicity label: Likely Oncogenic.
      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
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      17242690 ↗ C/EBPalphap30 plays transcriptional regulatory roles distinct from C/EBPalphap42. ONCOKB
      17671234 ↗ Target proteins of C/EBPalphap30 in AML: C/EBPalphap30 enhances sumoylation of C/EBPalphap42 via up-regulation of Ubc9. ONCOKB
      20884804 ↗ Two types of C/EBPα mutations play distinct but collaborative roles in leukemogenesis: lessons from clinical data and BMT models. ONCOKB
      31309149 ↗ Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML. ONCOKB
      31867767 ↗ Gain-of-Function Effects of N-Terminal CEBPA Mutations in Acute Myeloid Leukemia. ONCOKB