Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.865%, afr)
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 -1.7 | GERP -2.4 |
| Overall | ||
| CADD | 2.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.865%
African / African-American · 649/75,032 alleles
Filtering AF
0.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.788%
Overall
0.043%
694/1,614,158 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.865% | 116 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| Admixed American | 0.025% | 4,001 |
| European (non-Finnish) | 0.000424% | 236,007 |
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
- APOH
- Protein
- p.Ser159=
- Coding
- c.477A>G
- MANE Select
- NM_000042
- dbSNP
- rs8178925
- Type
- single nucleotide variant
- Location
- chr17:66220681 (GRCh38)
- Gene constraint
- LOEUF 1.542 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.16 · 14 PDB
- Residue 159
- a disulfide bond; the sushi 3 domain
Similar variants
- APOH c.64+8C>T Benign ★★ same type
- APOH p.Ala160Asp Benign ★★ same type
- APOH p.Arg154His Benign ★★ same type
- APOH p.Asn75Ser Benign ★★ same type
- APOH p.Pro53= Benign ★★ same type
- APOH p.Ala170Thr Uncertain significance ★ ⚠ same type
- APOH p.Ala179Val Uncertain significance ★ ⚠ same type
- APOH p.Ala230Thr 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/apoh-p-ser159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown