AFF2 p.Asp1152=
c.3456C>T · rs187306270 · VCV744002
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0313%, nfe)
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 0.78 | GERP -0.073, phastCons 1 |
| Overall | ||
| CADD | 7.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0313%
European (non-Finnish) · 278/887,622 alleles
Filtering AF
0.0283%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.0239%
287/1,201,639 alleles · ultra-rare
exomes 275/1,089,818 · genomes 12/111,821 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0313% | 3,193 |
| Remaining individualsnot grpmax-eligible | 0.0106% | 9,465 |
| Admixed American | 0.00437% | 22,873 |
| East Asian | 0.00296% | 33,736 |
| African / African-American | 0.00175% | 57,070 |
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.Asp1152=
- Coding
- c.3456C>T
- MANE Select
- NM_002025
- dbSNP
- rs187306270
- Type
- single nucleotide variant
- Location
- chrX:148977984 (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-asp1152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown