CNGA1 p.Ser157=
c.471G>A · rs369054249 · VCV2066154
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00907%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.26 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -8.3 |
| Overall | ||
| CADD | 0.164 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00907%
European (non-Finnish) · 107/1,179,674 alleles
Filtering AF
0.00766%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00709%
Overall
0.00713%
115/1,613,496 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00907% | 11,025 |
| East Asian | 0.00446% | 22,434 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| Admixed American | 0.00167% | 59,990 |
| Finnishnot grpmax-eligible | 0.00156% | 63,984 |
| African / African-American | 0.00134% | 74,848 |
| South Asian | 0.0011% | 91,062 |
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
- CNGA1
- Protein
- p.Ser157=
- Coding
- c.471G>A
- MANE Select
- NM_001379270
- dbSNP
- rs369054249
- Type
- single nucleotide variant
- Location
- chr4:47942115 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.88 · 19 PDB
Similar variants
- CNGA1 c.107+1G>A Likely pathogenic ★★ same type
- CNGA1 c.107+2T>G Likely pathogenic ★★ same type
- CNGA1 c.545+2T>A Likely pathogenic ★★ same type
- CNGA1 c.545+2T>C Likely pathogenic ★★ same type
- CNGA1 c.546-1G>C Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Arg214Ter Pathogenic ★★ same type
- CNGA1 p.Arg28Ter Pathogenic ★★ same type
- CNGA1 p.Arg420Ter Pathogenic/Likely pathogenic ★★ 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/cnga1-p-ser157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown