AFF4 p.Ser1079=
c.3237T>C · VCV3358028
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000678%, nfe)
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 4.7 | GERP 3.6, phastCons 1 |
| Overall | ||
| CADD | 8.583 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,180,022 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000496%
8/1,613,984 alleles · very rare
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.Ser1079=
- Coding
- c.3237T>C
- MANE Select
- NM_014423
- Type
- single nucleotide variant
- Location
- chr5:132883467 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62 · 9 PDB
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-ser1079 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown