AFF2 p.Pro98=
c.294A>G · rs370409032 · VCV728558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0479%, 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 2.4 | GERP -4.1, phastCons 1 |
| Overall | ||
| CADD | 9.212 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0479%
European (non-Finnish) · 428/894,351 alleles
Filtering AF
0.0441%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0426%
Overall
0.0383%
463/1,209,078 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0479% | 2,090 |
| Remaining individualsnot grpmax-eligible | 0.0462% | 2,162 |
| Middle Eastern | 0.0229% | 4,372 |
| Finnishnot grpmax-eligible | 0.015% | 6,660 |
| African / African-American | 0.00875% | 11,433 |
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.Pro98=
- Coding
- c.294A>G
- MANE Select
- NM_002025
- dbSNP
- rs370409032
- Type
- single nucleotide variant
- Location
- chrX:148662021 (GRCh38)
- Structure
- AlphaFold pLDDT 49.27
- Residue 98
- the 'disordered' region
Similar variants
- AFF2 p.Pro98Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown