COA7 p.Ala99=
c.297G>A · rs762820526 · VCV2178722
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -20 | |
| Overall | ||
| CADD | 0.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,884 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.00301%
44/1,461,446 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,442 |
| South Asian | 0.00439% | 22,772 |
| European (non-Finnish) | 0.00297% | 33,715 |
| African / African-American | 0.00267% | 37,516 |
| Finnishnot grpmax-eligible | 0.00157% | 63,566 |
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
- COA7
- Protein
- p.Ala99=
- Coding
- c.297G>A
- MANE Select
- NM_023077
- dbSNP
- rs762820526
- Type
- single nucleotide variant
- Location
- chr1:52688119 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 95.47 · 1 PDB
- Residue 99
- an α-helix
Similar variants
- COA7 p.Glu220Gln Uncertain significance ★★ ⚠ same type
- COA7 p.Glu31Lys Uncertain significance ★★ ⚠ same type
- COA7 p.Gly84Asp Uncertain significance ★★ ⚠ same type
- COA7 p.Tyr38Cys Uncertain significance ★★ ⚠ same type
- COA7 c.107-20C>G Benign/Likely benign ★★ same type
- COA7 c.107-5C>T Likely benign ★★ same type
- COA7 c.248-145C>T Benign ★★ same type
- COA7 c.248-36C>G 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/coa7-p-ala99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown