AFF2 p.Ser1149=
c.3447G>A · rs782742162 · VCV383413
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, mid)
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 -7 | GERP -3.5 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 5/4,336 alleles
Filtering AF
0.0454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0294%
Overall
0.00183%
22/1,204,879 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 867 |
| East Asian | 0.0207% | 4,822 |
| Remaining individualsnot grpmax-eligible | 0.00844% | 11,850 |
| African / African-American | 0.00525% | 19,042 |
| South Asian | 0.00353% | 28,338 |
| European (non-Finnish) | 0.000112% | 890,551 |
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.Ser1149=
- Coding
- c.3447G>A
- MANE Select
- NM_002025
- dbSNP
- rs782742162
- Type
- single nucleotide variant
- Location
- chrX:148977975 (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-ser1149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown