GNB3 p.Thr47=
c.141G>A · rs149095347 · VCV1168793
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0741%, 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 -9.1 | GERP -5 |
| Overall | ||
| CADD | 0.122 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0741%
African / African-American · 55/74,196 alleles
Filtering AF
0.0584%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0528%
Overall
0.00562%
88/1,565,184 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0741% | 1,349 |
| Middle Eastern | 0.0171% | 5,838 |
| Admixed American | 0.014% | 7,139 |
| Remaining individualsnot grpmax-eligible | 0.00497% | 20,110 |
| European (non-Finnish) | 0.00183% | 54,785 |
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
- GNB3
- Protein
- p.Thr47=
- Coding
- c.141G>A
- MANE Select
- NM_002075
- dbSNP
- rs149095347
- Type
- single nucleotide variant
- Location
- chr12:6843014 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.19 · 2 PDB
Similar variants
- GNB3 p.Thr47Met Uncertain significance ★ ⚠ same residue
- GNB3 p.Thr47_Arg48insThrAla Uncertain significance ★ same residue
- GNB3 c.203+6G>A Uncertain significance ★★ same type
- GNB3 p.Ala106Ser Uncertain significance ★★ ⚠ same type
- GNB3 p.Ala231Thr Uncertain significance ★★ ⚠ same type
- GNB3 p.Ala64Thr Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg129His Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg137Gln Uncertain significance ★★ ⚠ 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/gnb3-p-thr47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown