SBF1 p.Pro660=
c.1980G>A · rs143643893 · VCV787148
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.07%, afr)
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 -20 | GERP -5.2 |
| Overall | ||
| CADD | 1.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.07%
African / African-American · 1,550/75,032 alleles
Filtering AF
1.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.95%
Overall
0.114%
1,834/1,611,494 alleles · low-frequency
exomes 922/1,459,174 · genomes 912/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.07% | 48 |
| Remaining individualsnot grpmax-eligible | 0.197% | 508 |
| Admixed American | 0.187% | 533 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00552% | 18,125 |
| European (non-Finnish) | 0.00322% | 31,031 |
| East Asian | 0.00223% | 44,834 |
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.Pro660=
- Coding
- c.1980G>A
- MANE Select
- NM_002972
- dbSNP
- rs143643893
- Type
- single nucleotide variant
- Location
- chr22:50462706 (GRCh38)
- Gene constraint
- LOEUF 0.381 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
Similar variants
- SBF1 p.Pro660Leu Uncertain significance ★ ⚠ same residue
- SBF1 p.Pro660Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro660 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown