COA5 p.Ser28=
c.84G>C · rs1490818350 · VCV772204
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, 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 -0.2 | GERP -5.3, phastCons 0.17 |
| Overall | ||
| CADD | 10.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,834 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00131%
21/1,605,674 alleles · ultra-rare
exomes 20/1,453,420 · genomes 1/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,756 |
| Middle Eastern | 0.017% | 5,888 |
| Remaining individualsnot grpmax-eligible | 0.00966% | 10,348 |
| European (non-Finnish) | 8.5e-05% | 1,177,076 |
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.Ser28=
- Coding
- c.84G>C
- MANE Select
- NM_001008215
- dbSNP
- rs1490818350
- Type
- single nucleotide variant
- Location
- chr2:98608322 (GRCh38)
- Gene constraint
- LOEUF 1.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.42
- Residue 28
- the chch domain
Similar variants
- COA5 p.Ser28Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown