FOXA2 p.Ala103=
c.309C>T · rs1800847 · VCV1569424
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 18%, eas) — too common for a highly-penetrant pathogenic allele
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 -1.5 | GERP -4.5 |
| Overall | ||
| CADD | 5.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18%
East Asian · 7,246/40,346 alleles
Filtering AF
17.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.5%
Overall
5.02%
76,729/1,528,470 alleles · common
exomes 64,568/1,376,450 · genomes 12,161/152,020 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 18% | 6 |
| African / African-American | 16.6% | 6 |
| Amishnot grpmax-eligible | 12.7% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 9.12% | 11 |
| South Asian | 8.39% | 12 |
| Remaining individualsnot grpmax-eligible | 6.45% | 16 |
| Middle Eastern | 5.88% | 17 |
| Admixed American | 3.68% | 27 |
| European (non-Finnish) | 3.58% | 28 |
| Finnishnot grpmax-eligible | 2.66% | 38 |
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
- FOXA2
- Protein
- p.Ala103=
- Coding
- c.309C>T
- MANE Select
- NM_021784
- dbSNP
- rs1800847
- Type
- single nucleotide variant
- Location
- chr20:22582933 (GRCh38)
- Gene constraint
- LOEUF 0.518 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 58.29 · 3 PDB
Similar variants
- FOXA2 p.Ala92Val Uncertain significance ★★ ⚠ same type
- FOXA2 p.Glu373Asp Uncertain significance ★★ ⚠ same type
- FOXA2 p.Met108Ile Uncertain significance ★★ ⚠ same type
- FOXA2 p.Met52Thr Uncertain significance ★★ same type
- FOXA2 p.Pro358Gln Uncertain significance ★★ ⚠ same type
- FOXA2 p.Ser99Leu Uncertain significance ★★ ⚠ same type
- FOXA2 c.*6C>T Likely benign ★★ same type
- FOXA2 p.Ala100Pro Benign/Likely benign ★★ 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/foxa2-p-ala103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown