Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.942%, 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 -6.3 | GERP -4.7 |
| Overall | ||
| CADD | 0.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.942%
African / African-American · 707/75,026 alleles
Filtering AF
0.885%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.862%
Overall
0.059%
952/1,613,864 alleles · rare
exomes 552/1,461,640 · genomes 400/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.942% | 106 |
| Middle Eastern | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.0976% | 1,025 |
| Admixed American | 0.08% | 1,250 |
| South Asian | 0.0143% | 7,006 |
| European (non-Finnish) | 0.00975% | 10,260 |
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
- GOLGA3
- Protein
- p.Ser282=
- Coding
- c.846C>T
- MANE Select
- NM_001389683
- dbSNP
- rs7299219
- Type
- single nucleotide variant
- Location
- chr12:132808223 (GRCh38)
- Gene constraint
- LOEUF 0.568 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76
- Residue 282
- the 'disordered' region
Similar variants
- GOLGA3 p.Ala563Val Benign ★★ same type
- GOLGA3 c.2812-1G>A Uncertain significance ★ same type
- GOLGA3 p.Ala1015Val Uncertain significance ★ ⚠ same type
- GOLGA3 p.Ala1019Pro Uncertain significance ★ ⚠ same type
- GOLGA3 p.Ala1019Thr Uncertain significance ★ ⚠ same type
- GOLGA3 p.Ala1022Thr Uncertain significance ★ ⚠ same type
- GOLGA3 p.Ala1029Val Uncertain significance ★ ⚠ same type
- GOLGA3 p.Ala1070Val 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/golga3-p-ser282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown