AFF1 p.Asp189=
c.567C>T · rs143673312 · VCV716818
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0357%, eas)
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 -5.8 | GERP -4.2 |
| Overall | ||
| CADD | 3.706 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0357%
East Asian · 16/44,880 alleles
Filtering AF
0.0223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00285%
46/1,614,174 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0357% | 2,805 |
| African / African-American | 0.0293% | 3,411 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
| South Asian | 0.0022% | 45,541 |
| Admixed American | 0.00167% | 60,026 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Asp189=
- Coding
- c.567C>T
- MANE Select
- NM_001166693
- dbSNP
- rs143673312
- Type
- single nucleotide variant
- Location
- chr4:87047102 (GRCh38)
- Gene constraint
- LOEUF 0.49 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06 · 1 PDB
- Residue 189
- the 'disordered' region
Similar variants
- AFF1 c.1191+8C>T Benign/Likely benign ★★ same type
- AFF1 p.Ala40= Benign ★★ same type
- AFF1 p.Pro393= 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
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-asp189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown