COA7 p.Ala2=
c.6C>T · rs374935492 · VCV2896732
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, 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 -1.7 | GERP -4.9 |
| Overall | ||
| CADD | 2.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
Admixed American · 15/59,960 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.00919%
148/1,609,940 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.025% | 3,997 |
| European (non-Finnish) | 0.0106% | 9,432 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,598 |
| African / African-American | 0.00535% | 18,701 |
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.Ala2=
- Coding
- c.6C>T
- MANE Select
- NM_023077
- dbSNP
- rs374935492
- Type
- single nucleotide variant
- Location
- chr1:52698321 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 95.47 · 1 PDB
- Residue 2
- a modified residue (n-acetylalanine)
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-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown