OSBPL2 p.Ser72=
c.216C>T · rs35907950 · VCV667054
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.04%, 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 -7 | GERP -5.1 |
| Overall | ||
| CADD | 3.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.04%
African / African-American · 3,028/75,020 alleles
Filtering AF
3.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.87%
Overall
0.206%
3,325/1,614,134 alleles · low-frequency
exomes 1,579/1,461,836 · genomes 1,746/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.04% | 25 |
| Remaining individualsnot grpmax-eligible | 0.206% | 485 |
| Admixed American | 0.172% | 583 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.011% | 9,108 |
| European (non-Finnish) | 0.00398% | 25,107 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,878 |
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
- OSBPL2
- Protein
- p.Ser72=
- Coding
- c.216C>T
- MANE Select
- NM_144498
- dbSNP
- rs35907950
- Type
- single nucleotide variant
- Location
- chr20:62263649 (GRCh38)
- Gene constraint
- LOEUF 0.467 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.92 · 1 PDB
Similar variants
- OSBPL2 p.Ala442Val Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Arg434Trp Uncertain significance ★★ same type
- OSBPL2 p.Asp475Asn Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gln125Pro Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gln58Pro Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Glu284Gly Uncertain significance ★★ same type
- OSBPL2 p.Gly149Ser Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gly245Arg 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/osbpl2-p-ser72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown