APOO c.117+16T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 51.8%, afr) — 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 | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP 0.48, phastCons 0.003 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 5.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
51.8%
African / African-American · 27,745/53,574 alleles
Filtering AF
51.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 51.1%
Overall
19.9%
216,688/1,089,686 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 51.8% | 2 |
| South Asian | 24.9% | 4 |
| Admixed American | 23.1% | 4 |
| Middle Eastern | 20.9% | 5 |
| Remaining individualsnot grpmax-eligible | 20.6% | 5 |
| Amishnot grpmax-eligible | 19.1% | 5 |
| Finnishnot grpmax-eligible | 18.2% | 5 |
| European (non-Finnish) | 17.7% | 6 |
| East Asian | 16.5% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 14% | 7 |
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
- APOO
- Coding
- c.117+16T>C
- MANE Select
- NM_024122
- dbSNP
- rs16982839
- Type
- single nucleotide variant
- Location
- chrX:23880829 (GRCh38)
- Structure
- AlphaFold pLDDT 74.34
Similar variants
- APOO p.Leu166Val Benign ★★ same type
- APOO p.Ile117Thr Pathogenic ★ ⚠ same type
- APOO p.Ala12Gly Uncertain significance ★ ⚠ same type
- APOO p.Asp98Glu Uncertain significance ★ ⚠ same type
- APOO p.Glu72Lys Uncertain significance ★ ⚠ same type
- APOO p.Gly163Ala Uncertain significance ★ ⚠ same type
- APOO p.Gly173Glu Uncertain significance ★ ⚠ same type
- APOO p.Ile133Met 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/apoo-c-117-plus-16t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown