AFF1 p.Pro393=
c.1179T>C · rs113502077 · VCV786038
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.3%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.058, phastCons 1 |
| Overall | ||
| CADD | 8.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
African / African-American · 225/75,064 alleles
Filtering AF
0.268%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.255%
Overall
0.0199%
321/1,613,740 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.3% | 334 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.0516% | 1,936 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| European (non-Finnish) | 0.00229% | 43,693 |
| South Asian | 0.0011% | 91,072 |
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
- AFF1
- Protein
- p.Pro393=
- Coding
- c.1179T>C
- MANE Select
- NM_001166693
- dbSNP
- rs113502077
- Type
- single nucleotide variant
- Location
- chr4:87090058 (GRCh38)
- Gene constraint
- LOEUF 0.49 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06 · 1 PDB
- Residue 393
- the 'disordered' region
Similar variants
- AFF1 c.1191+8C>T Benign/Likely benign ★★ same type
- AFF1 p.Ala40= Benign ★★ same type
- AFF1 p.Ser627Cys Likely benign ★★ ⚠ same type
- AFF1 p.Thr426= Likely benign ★★ same type
- AFF1 p.Val711Ile Benign ★★ same type
- AFF1 p.Ala1047Val Uncertain significance ★ ⚠ same type
- AFF1 p.Ala1103Thr Uncertain significance ★ ⚠ same type
- AFF1 p.Ala127Val 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/aff1-p-pro393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown