AFF4 p.Ala939=
c.2817T>C · rs140405448 · VCV1338148
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, 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 -1.7 | GERP -7.8 |
| Overall | ||
| CADD | 5.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,924 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000372%
6/1,613,634 alleles · very rare
exomes 1/1,461,422 · genomes 5/152,212 · joint denominator
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
- AFF4
- Protein
- p.Ala939=
- Coding
- c.2817T>C
- MANE Select
- NM_014423
- dbSNP
- rs140405448
- Type
- single nucleotide variant
- Location
- chr5:132887962 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62 · 9 PDB
- Residue 939
- an α-helix
Similar variants
- AFF4 p.Arg258Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- AFF4 p.Met260Val Likely pathogenic ★★ ⚠ same type
- AFF4 p.Pro253Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- AFF4 p.Thr254Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- AFF4 c.1133+3A>G Uncertain significance ★★ same type
- AFF4 p.Ala114Thr Uncertain significance ★★ ⚠ same type
- AFF4 p.Ala114Val Uncertain significance ★★ ⚠ same type
- AFF4 p.Ala27Thr 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/aff4-p-ala939 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown