AFF4 p.Lys924=
c.2772G>A · VCV3351350
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00335%, amr)
Conditions
1
AFF4-related disorder
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 0.14 | GERP 0.015, phastCons 0.9 |
| Overall | ||
| CADD | 6.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
Admixed American · 2/59,790 alleles
Filtering AF
0.000555%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000208%
Overall
0.000372%
6/1,610,852 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00335% | 29,895 |
| European (non-Finnish) | 0.000339% | 294,555 |
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.Lys924=
- Coding
- c.2772G>A
- MANE Select
- NM_014423
- Type
- single nucleotide variant
- Location
- chr5:132888121 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62 · 9 PDB
- Residue 924
- an α-helix
Disease context
AFF4-related disorder
Similar variants
- AFF4 p.Glu657Asp Uncertain significance ★★ ⚠ same condition
- AFF4 p.Ser839Cys Uncertain significance ★★ ⚠ same condition
- AFF4 p.Ala551Thr Uncertain significance ★ ⚠ same condition
- AFF4 p.Arg209Ser Uncertain significance ★ ⚠ same condition
- AFF4 p.Arg725Lys Uncertain significance ★ ⚠ same condition
- AFF4 p.Asp422Gly Uncertain significance ★ ⚠ same condition
- AFF4 p.Pro611Leu Uncertain significance ★ ⚠ same condition
- AFF4 p.Ser1077Phe Uncertain significance ★ ⚠ same condition
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-lys924 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown