AFF2 p.Thr1279=
c.3837G>A · rs61743576 · VCV128284
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.9%, 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 -1.9 | GERP -3.9 |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.9%
African / African-American · 2,793/57,039 alleles
Filtering AF
4.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.68%
Overall
0.529%
6,369/1,204,874 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.9% | 20 |
| South Asian | 4.33% | 23 |
| Middle Eastern | 1.04% | 96 |
| Remaining individualsnot grpmax-eligible | 0.844% | 118 |
| Admixed American | 0.372% | 269 |
| European (non-Finnish) | 0.0566% | 1,766 |
| Finnishnot grpmax-eligible | 0.0538% | 1,860 |
| East Asian | 0.0209% | 4,789 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00456% | 21,918 |
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
- AFF2
- Protein
- p.Thr1279=
- Coding
- c.3837G>A
- MANE Select
- NM_002025
- dbSNP
- rs61743576
- Type
- single nucleotide variant
- Location
- chrX:148991233 (GRCh38)
- Structure
- AlphaFold pLDDT 49.27
Similar variants
- AFF2 c.3267+5G>C Uncertain significance ★★ same type
- AFF2 p.Ala1197Thr Uncertain significance ★★ ⚠ same type
- AFF2 p.Ala171Pro Uncertain significance ★★ ⚠ same type
- AFF2 p.Arg1238Cys Uncertain significance ★★ ⚠ same type
- AFF2 p.Arg1295Cys Uncertain significance ★★ ⚠ same type
- AFF2 p.Arg670His Uncertain significance ★★ ⚠ same type
- AFF2 p.Asn77Ile Uncertain significance ★★ ⚠ same type
- AFF2 p.Asp187Glu 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/aff2-p-thr1279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown