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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 applied · 17 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
Frameshift variant NM_004364.3:c.47_48delinsA (p.Ser16LysfsTer144) in exon 1 of CEBPA, a gene where loss-of-function is an established mechanism for autosomal dominant familial acute myeloid leukemia predisposition. The variant is predicted to cause premature termination at codon 159, ablating expression of the full-length p42 isoform. Germline loss-of-function disease mechanism confirmed by literature review supporting CEBPA as a germline predisposition gene (WHO 5th edition myeloid neoplasm classification). Assessed under ClinGen SVI PVS1 framework (PMC6185798).
Frameshift null variant at codon 16 of 359 in a gene with established germline loss-of-function disease mechanismVariant predicted to produce p.Ser16LysfsTer144abolishing full-length p42 CEBPA isoform expression
PM2 supporting Pathogenic
Variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases, consistent with a rare pathogenic variant. Under generic ACMG/AMP 2015 rules, PM2 is met at supporting strength (allele frequency <0.1%).
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0 (genomes)
Assessed · not applied
Pathogenic
PS2 No de novo data available for this variant.
PS3 Five papers on N-terminal CEBPA mutations and p30 isoform function were reviewed in full text or abstract.
PS4 No case-control data or prevalence comparison available for this variant.
PM1 Variant does not lie in a statistically significant mutational hotspot as assessed by cancerhotspots.org.
PM6 No de novo data with or without confirmed maternity/paternity available for this variant.
PP1 No cosegregation data available for this variant.
PP3 SpliceAI predicts no splice-altering effect (max delta score = 0.00).
PP4 No patient phenotype data available to assess specificity of clinical presentation.
PP5 Variant is absent from ClinVar and has not been classified by any germline diagnostic laboratory or expert panel.
Benign
BA1 Variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).
BS1 Variant is absent from all population databases.
BS2 No data on observation of this variant in healthy adults available.
BS3 Five papers on CEBPA N-terminal mutations were reviewed (full text for PMID:31309149 and PMID:31867767; abstracts for PMID:17242690, 17671234, 20884804).
BS4 No segregation data available.
BP2 No data on observation of this variant in trans with a known pathogenic variant.
BP5 No data on observation of this variant in a case with an alternate molecular basis for disease.
BP6 Variant is absent from ClinVar and has not been classified as benign or likely benign by any reputable source.
N/A · 9 PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP4 · BP7
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/EBP&#x3b1; 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