Genetic Information
Gene & Transcript Details
Gene
DNMT3A
Transcript
NM_022552.4
MANE Select
Total Exons
—
Reference Sequence
NC_000002.11
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_022552.4 | RefSeq Select | 4324 nt | 268–3006 |
| NM_022552.5 | MANE Select | 9421 nt | 278–3016 |
| NM_022552.3 | Alternative | 4314 nt | 258–2996 |
Variant Details
HGVS Notation
NM_022552.4:c.1475-19C>T
Protein Change
?
Location
Exon 12
(Exon 12 of )
12
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
0.000807 in 100,000
Extremely Rare
ACMG Criteria Applied
PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).
ClinVar
OpenClassification
Likely Benign
1 publications
Clinical Statement
"This variant has been reported in ClinVar as Likely benign (1 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
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Functional Impact & Domains
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene DNMT3A.
Functional Summary
Error in OpenAI Consolidation. OncoKB: DNMT3A1475-19C>TDNMT3A1475-19C>TSomaticNCBI Gene:1788|Show additional gene information Variant OverviewDNMT3A, a tumor suppressor and DNA methyltransferase, is recurrently mutated in acute myeloid leukemia and other hematologic malignancies.The DNMT3A 1475-19c>T mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found
Database Previews
OncoKB
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.0 | 218 bp |
| Donor Loss (DL) | 0.0 | -453 bp |
| Acceptor Gain (AG) | 0.0 | 221 bp |
| Donor Gain (DG) | 0.0 | 219 bp |
High impact (≥0.5)
Medium impact (0.2-0.49)
Low impact (<0.2)
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
Filter Criteria:
PM2
PM2 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP4
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP6
BP6 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)