DDB2 c.702+4C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -4.6 |
| Non-coding constraint | Z 2.48 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 13.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,080 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00273%
44/1,613,972 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,385 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| Admixed American | 0.005% | 19,999 |
| European (non-Finnish) | 0.00237% | 42,139 |
| East Asian | 0.00223% | 44,872 |
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
- DDB2
- Coding
- c.702+4C>T
- MANE Select
- NM_000107
- dbSNP
- rs367648586
- Type
- single nucleotide variant
- Location
- chr11:47234676 (GRCh38)
- Gene constraint
- LOEUF 0.719 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.69 · 10 PDB
Similar variants
- DDB2 c.702+1G>T Pathogenic/Likely pathogenic ★★ same type
- DDB2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- DDB2 p.Arg273His Pathogenic/Likely pathogenic ★★ ⚠ same type
- DDB2 p.Arg355Ter Pathogenic ★★ same type
- DDB2 p.Arg332His Uncertain significance ★★ ⚠ same type
- DDB2 p.Cys66Gly Uncertain significance ★★ ⚠ same type
- DDB2 p.Glu178Ala Uncertain significance ★★ ⚠ same type
- DDB2 p.Leu350Pro 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/ddb2-c-702-plus-4c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown