COA5 p.Lys8=
c.24G>A · rs771021752 · VCV2816140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00169%, amr)
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 0.78 | GERP -0.31, phastCons 1 |
| Overall | ||
| CADD | 12.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00169%
Admixed American · 1/59,132 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000832%
Overall
0.00131%
21/1,604,948 alleles · very rare
exomes 21/1,452,570 · genomes 0/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00169% | 59,132 |
| European (non-Finnish) | 0.00161% | 61,950 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,146 |
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
- COA5
- Protein
- p.Lys8=
- Coding
- c.24G>A
- MANE Select
- NM_001008215
- dbSNP
- rs771021752
- Type
- single nucleotide variant
- Location
- chr2:98608382 (GRCh38)
- Gene constraint
- LOEUF 1.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.42
Similar variants
- COA5 p.Ala53Thr Uncertain significance ★★ ⚠ same type
- COA5 p.Ala66Val Uncertain significance ★★ ⚠ same type
- COA5 c.100-239A>G Benign ★★ same type
- COA5 c.100-53A>G Benign ★★ same type
- COA5 c.99+28G>A Benign ★★ same type
- COA5 c.-130G>C Benign ★★ same type
- COA5 c.-69C>G Likely benign ★★ same type
- COA5 c.-71C>T Likely benign ★★ 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/coa5-p-lys8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown