DMAP1 c.1344+3A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.63%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.27 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 0.58, phastCons 1 |
| Non-coding constraint | Z 2.15 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 16.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.63%
African / African-American · 462/73,336 alleles
Filtering AF
0.583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.564%
Overall
0.0333%
513/1,540,746 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.63% | 159 |
| Admixed American | 0.0555% | 1,802 |
| Remaining individualsnot grpmax-eligible | 0.0287% | 3,483 |
| South Asian | 0.00126% | 79,560 |
| European (non-Finnish) | 0.000351% | 284,982 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DMAP1
- Coding
- c.1344+3A>G
- MANE Select
- NM_019100
- dbSNP
- rs140100133
- Type
- single nucleotide variant
- Location
- chr1:44220312 (GRCh38)
- Gene constraint
- LOEUF 0.691 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.46 · 18 PDB
Similar variants
- DMAP1 p.Arg224Ter Uncertain significance ★★ same type
- DMAP1 p.Arg283His Uncertain significance ★★ ⚠ same type
- DMAP1 p.Tyr196Ser Uncertain significance ★★ ⚠ same type
- DMAP1 p.Arg226Trp Likely pathogenic ★ same type
- DMAP1 c.394-1G>C Uncertain significance ★ same type
- DMAP1 p.Ala207Thr Uncertain significance ★ ⚠ same type
- DMAP1 p.Ala2Thr Uncertain significance ★ ⚠ same type
- DMAP1 p.Ala411Pro Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dmap1-c-1344-plus-3a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown