Starting
Initialising…
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DNMT3A
Final classification
VUS
DNMT3A c.2395C>T · p.Pro799Ser
DNMT3A

This variant is a missense substitution (c.2395C>T, p.Pro799Ser) in exon 20 of DNMT3A (NM_022552.4). It is absent from ClinVar and has an extremely low allele frequency in gnomAD v4.1 (4/1,613,986 alleles; AF=0.00025%), meeting PM2 (supporting). In silico prediction tools support a deleterious effect (REVEL=0.916; BayesDel=0.504), meeting PP3 (supporting). SpliceAI predicts no significant splicing alteration (max delta=0.04).

Gene
DNMT3A
Transcript
NM_022552.4
HGVS · transcript:coding
NM_022552.4:c.2395C>T
Consequence
N/A
GRCh38
chr2:25239143 G>A
GRCh37
chr2:25462012 G>A
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, PP3 supporting; combination = 2 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, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
DNMT3A c.2395C>T

This variant is a missense substitution (c.2395C>T, p.Pro799Ser) in exon 20 of DNMT3A (NM_022552.4). It is absent from ClinVar and has an extremely low allele frequency in gnomAD v4.1 (4/1,613,986 alleles; AF=0.00025%), meeting PM2 (supporting). In silico prediction tools support a deleterious effect (REVEL=0.916; BayesDel=0.504), meeting PP3 (supporting). SpliceAI predicts no significant splicing alteration (max delta=0.04).1 No variant-specific functional data, de novo observations, case-control enrichment, segregation data, or clinical phenotype information are available for this variant. Two publications (PMID:24345752 and PMID:34429321) were identified as potentially relevant but neither could be verified to contain this exact variant (NM_022552.4:c.2395C>T/p.Pro799Ser). PVS1 does not apply to this missense variant. No same-residue comparator variants (PM5) were identified. The variant has been observed once in COSMIC (COSV104391761) as a somatic finding.2 With PM2 (supporting) and PP3 (supporting) as the only met criteria, the evidence does not reach any classification threshold under the generic ACMG/AMP 2015 combination rules (PMID:25741868). Two supporting criteria alone are insufficient for Likely Pathogenic (requires ≥1 moderate + 4 supporting or stronger combinations). This variant is classified as a Variant of Uncertain Significance (VUS). Review of full-text PMID:34429321 (Huang et al., systematic DNMT3A variant profiling) is recommended, as it may contain functional data for Pro799Ser that could upgrade PS3/BS3 status.3

PM2 + PP3 VUS
3 generic_acmg_combination_rules
Gene diagram · NM_022552.4 · variants mapped to exon structure
DNMT3A NM_022552.4
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
      This variant is present in gnomAD v4.1 (AF= 2.47834e-06; MAF= 0.00025%, 4/1613986 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.39009e-06; MAF= 0.00034%, 4/1179910 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00025% · 4 / 1,613,986
      0 hom · FAF 7.9e-05%
      European (non-Finnish)
      4 / 1,179,910
      0.00034%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 = 0.04). REVEL score = 0.916. BayesDel score = 0.504786.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. DNMT3A, a tumor suppressor and DNA methyltransferase, is recurrently mutated in acute myeloid leukemia and other hematologic malignancies.
      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 previously been reported in somatic cancers (COSMIC; COSV104391761, n = 1 times).
      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
      Triaged references · 2 PMIDs not cited in assessment
      24345752 ↗ A targeted mutational landscape of angioimmunoblastic T-cell lymphoma. ONCOKB
      34429321 ↗ Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor. ONCOKB