AFP p.Ser286=
c.858C>T · rs28482344 · VCV771142
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.78%, 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 -0.89 | GERP -3.6 |
| Overall | ||
| CADD | 2.978 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.78%
European (non-Finnish) · 20,902/1,176,888 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.75%
Overall
1.43%
23,011/1,608,108 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.78% | 56 |
| Remaining individualsnot grpmax-eligible | 1.29% | 77 |
| Middle Eastern | 0.824% | 121 |
| Admixed American | 0.659% | 152 |
| Finnishnot grpmax-eligible | 0.443% | 225 |
| South Asian | 0.337% | 296 |
| African / African-American | 0.297% | 336 |
| Ashkenazi Jewishnot grpmax-eligible | 0.18% | 556 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| East Asian | 0.00669% | 14,940 |
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
- AFP
- Protein
- p.Ser286=
- Coding
- c.858C>T
- MANE Select
- NM_001134
- dbSNP
- rs28482344
- Type
- single nucleotide variant
- Location
- chr4:73447476 (GRCh38)
- Gene constraint
- LOEUF 0.963 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.83 · 5 PDB
- Residue 286
- the albumin 2 domain; an α-helix
Similar variants
- AFP c.714-5C>T Likely benign ★★ same type
- AFP p.Ser445= Benign ★★ same type
- AFP p.Gly608Arg Likely pathogenic ★ ⚠ same type
- AFP p.Ala134Val Uncertain significance ★ ⚠ same type
- AFP p.Ala471Val Uncertain significance ★ ⚠ same type
- AFP p.Ala476Thr Uncertain significance ★ ⚠ same type
- AFP p.Ala476Val Uncertain significance ★ ⚠ same type
- AFP p.Ala605Ser 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/afp-p-ser286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown