CHRNA7 p.Pro399=
c.1197G>C · rs200858080 · VCV1177915
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.961%, 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 -5.1 | GERP -2.8 |
| Overall | ||
| CADD | 0.376 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.961%
African / African-American · 703/73,174 alleles
Filtering AF
0.902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.878%
Overall
0.0501%
796/1,589,740 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.961% | 104 |
| Remaining individualsnot grpmax-eligible | 0.0765% | 1,307 |
| Admixed American | 0.0605% | 1,653 |
| Middle Eastern | 0.02% | 5,002 |
| South Asian | 0.0057% | 17,546 |
| European (non-Finnish) | 0.000427% | 234,027 |
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
- CHRNA7
- Protein
- p.Pro399=
- Coding
- c.1197G>C
- MANE Select
- NM_000746
- dbSNP
- rs200858080
- Type
- single nucleotide variant
- Location
- chr15:32168146 (GRCh38)
- Gene constraint
- LOEUF 1.064 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.16 · 51 PDB
Similar variants
- CHRNA7 p.Asn381Asp Uncertain significance ★★ ⚠ same type
- CHRNA7 p.Val374Met Uncertain significance ★★ ⚠ same type
- CHRNA7 c.196-4G>T Likely benign ★★ same type
- CHRNA7 c.240+113C>A Benign ★★ same type
- CHRNA7 c.350+304G>A Likely benign ★★ same type
- CHRNA7 c.55+77G>A Benign ★★ same type
- CHRNA7 c.598+86C>T Benign ★★ same type
- CHRNA7 c.599-111T>A 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/chrna7-p-pro399 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown