DONSON c.402+52C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 74%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +52 | deep intronic (+52 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.11 | GERP -2.2, phastCons 0.001 |
| Non-coding constraint | Z 0.30 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 2.157 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
74%
African / African-American · 51,850/70,094 alleles
Filtering AF
73.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 73.2%
Overall
68.1%
1,019,415/1,497,522 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 74% | 1 |
| East Asian | 73.7% | 1 |
| Finnishnot grpmax-eligible | 69.5% | 1 |
| Amishnot grpmax-eligible | 68.4% | 1 |
| European (non-Finnish) | 67.9% | 1 |
| Admixed American | 67.7% | 1 |
| Remaining individualsnot grpmax-eligible | 67.7% | 1 |
| South Asian | 65.2% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 58.2% | 2 |
| Middle Eastern | 57.3% | 2 |
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
- DONSON
- Coding
- c.402+52C>T
- MANE Select
- NM_017613
- dbSNP
- rs7283856
- Type
- single nucleotide variant
- Location
- chr21:33587470 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.94
Similar variants
- DONSON c.1047-9A>G Pathogenic ★★ same type
- DONSON c.1563+1G>T Pathogenic ★★ same type
- DONSON p.Arg293Ter Pathogenic ★★ same type
- DONSON p.Arg442Ter Pathogenic ★★ same type
- DONSON p.Gln428Ter Pathogenic/Likely pathogenic ★★ same type
- DONSON p.Phe165Ser Pathogenic/Likely pathogenic ★★ same type
- DONSON p.Ala32Gly Uncertain significance ★★ ⚠ same type
- DONSON p.Ala429Glu 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/donson-c-402-plus-52c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown