ACTN3 p.Ala470=
c.1410G>A · rs114371258 · VCV3034423
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.06%, 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 -2.6 | GERP -5.1 |
| Overall | ||
| CADD | 5.805 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.06%
African / African-American · 1,443/69,972 alleles
Filtering AF
1.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.94%
Overall
0.116%
1,791/1,548,950 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.06% | 48 |
| Admixed American | 0.301% | 332 |
| Remaining individualsnot grpmax-eligible | 0.22% | 454 |
| Middle Eastern | 0.0671% | 1,491 |
| South Asian | 0.0108% | 9,281 |
| European (non-Finnish) | 0.0052% | 19,231 |
| Finnishnot grpmax-eligible | 0.00323% | 30,976 |
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
- ACTN3
- Protein
- p.Ala470=
- Coding
- c.1410G>A
- MANE Select
- NM_001104
- dbSNP
- rs114371258
- Type
- single nucleotide variant
- Location
- chr11:66559369 (GRCh38)
- Gene constraint
- LOEUF 0.944 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.61 · 3 PDB
Similar variants
- ACTN3 p.Ala470Pro Uncertain significance ★ ⚠ same residue
- ACTN3 p.Ala115Asp Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala149Thr Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala251Thr Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala410Pro Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala410Val Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala460Val Uncertain significance ★ ⚠ same type
- ACTN3 p.Ala469Gly 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/actn3-p-ala470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown