CHRNA7 p.Ser15=
c.45G>A · rs200390587 · VCV710974
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.352%, mid)
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 1.3 | GERP -0.037, phastCons 1 |
| Overall | ||
| CADD | 12.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.352%
Middle Eastern · 19/5,394 alleles
Filtering AF
0.263%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.252%
Overall
0.0356%
559/1,572,036 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.352% | 284 |
| South Asian | 0.293% | 341 |
| Remaining individualsnot grpmax-eligible | 0.0296% | 3,380 |
| European (non-Finnish) | 0.022% | 4,548 |
| Admixed American | 0.0176% | 5,682 |
| African / African-American | 0.00559% | 17,899 |
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.Ser15=
- Coding
- c.45G>A
- MANE Select
- NM_000746
- dbSNP
- rs200390587
- Type
- single nucleotide variant
- Location
- chr15:32030639 (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-ser15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown