DPM2 c.3+99C>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.32%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +99 | deep intronic (+99 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.046 | GERP -3.3 |
| Overall | ||
| CADD | 5.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.32%
African / African-American · 961/72,610 alleles
Filtering AF
1.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.23%
Overall
0.0719%
1,073/1,492,268 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.32% | 76 |
| Remaining individualsnot grpmax-eligible | 0.101% | 990 |
| Admixed American | 0.072% | 1,388 |
| Middle Eastern | 0.0344% | 2,904 |
| South Asian | 0.00113% | 88,594 |
| European (non-Finnish) | 0.000655% | 152,768 |
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
- DPM2
- Coding
- c.3+99C>G
- MANE Select
- NM_003863
- dbSNP
- rs73669305
- Type
- single nucleotide variant
- Location
- chr9:127937719 (GRCh38)
- Gene constraint
- LOEUF 1.274 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.96
Similar variants
- DPM2 p.Arg47Ter Pathogenic/Likely pathogenic ★★ same type
- DPM2 p.Ala52Thr Uncertain significance ★★ ⚠ same type
- DPM2 p.Leu30Val Uncertain significance ★★ ⚠ same type
- DPM2 p.Leu62Val Uncertain significance ★★ ⚠ same type
- DPM2 p.Tyr43His Uncertain significance ★★ ⚠ same type
- DPM2 p.Val51Ile Uncertain significance ★★ ⚠ same type
- DPM2 c.196+191C>G Likely benign ★★ same type
- DPM2 c.3+12A>G Benign/Likely benign ★★ 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/dpm2-c-3-plus-99c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown