APOC3 p.Ala16=
c.48C>T · rs774247573 · VCV1743950
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
Conditions
1
Cardiovascular phenotype
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 0.051 | GERP 0.37, phastCons 0.25 |
| Overall | ||
| CADD | 9.317 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,920 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000682%
11/1,613,836 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,487 |
| Admixed American | 0.00167% | 60,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000254% | 393,335 |
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
- APOC3
- Protein
- p.Ala16=
- Coding
- c.48C>T
- MANE Select
- NM_000040
- dbSNP
- rs774247573
- Type
- single nucleotide variant
- Location
- chr11:116830630 (GRCh38)
- Gene constraint
- LOEUF 1.68 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.90 · 1 PDB
Similar variants
- APOC3 p.Glu24Lys Uncertain significance ★★ ⚠ same condition
- APOC3 p.Leu14Phe Uncertain significance ★★ ⚠ same condition
- APOC3 p.Val91Ile Uncertain significance ★★ ⚠ same condition
- APOC3 p.Ala23= Benign/Likely benign ★★ same condition
- APOC3 p.Gln33= Benign/Likely benign ★★ same condition
- APOC3 p.Gly34= Benign ★★ same condition
- APOC3 p.His38= Likely benign ★★ same condition
- APOC3 p.Thr42= Benign/Likely benign ★★ same condition
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/apoc3-p-ala16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown