SBF1 p.Ala587=
c.1761C>T · rs766048226 · VCV1604726
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00693%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -4.9 |
| Overall | ||
| CADD | 1.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00693%
East Asian · 3/43,268 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00533%
84/1,575,932 alleles · very rare
exomes 81/1,423,680 · genomes 3/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00693% | 14,423 |
| Remaining individualsnot grpmax-eligible | 0.00656% | 15,237 |
| European (non-Finnish) | 0.00647% | 15,456 |
| Admixed American | 0.00184% | 54,438 |
| South Asian | 0.00114% | 87,490 |
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
- SBF1
- Protein
- p.Ala587=
- Coding
- c.1761C>T
- MANE Select
- NM_002972
- dbSNP
- rs766048226
- Type
- single nucleotide variant
- Location
- chr22:50463421 (GRCh38)
- Gene constraint
- LOEUF 0.381 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
Similar variants
- SBF1 c.3826+1G>A Pathogenic/Likely pathogenic ★★ same type
- SBF1 p.Met417Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- SBF1 c.1431+6A>T Uncertain significance ★★ same type
- SBF1 c.1636+4C>T Uncertain significance ★★ same type
- SBF1 c.1899+3G>A Uncertain significance ★★ same type
- SBF1 c.2643+6C>T Uncertain significance ★★ same type
- SBF1 c.279+3C>T Uncertain significance ★★ same type
- SBF1 c.3904+6G>A 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/sbf1-p-ala587 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown