Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.17%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.088 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP 0.11, phastCons 0.93 |
| Overall | ||
| CADD | 5.153 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.17%
East Asian · 2,302/44,524 alleles
Filtering AF
4.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.92%
Overall
0.252%
3,980/1,581,758 alleles · common
exomes 3,390/1,429,538 · genomes 590/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.17% | 19 |
| Admixed American | 1.62% | 62 |
| Remaining individualsnot grpmax-eligible | 0.309% | 324 |
| South Asian | 0.153% | 653 |
| Ashkenazi Jewishnot grpmax-eligible | 0.117% | 855 |
| African / African-American | 0.0645% | 1,550 |
| Finnishnot grpmax-eligible | 0.0409% | 2,443 |
| European (non-Finnish) | 0.0242% | 4,138 |
| Middle Eastern | 0.0168% | 5,946 |
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
- VPS50
- Protein
- p.Pro896=
- Coding
- c.2688C>G
- MANE Select
- NM_017667
- dbSNP
- rs3764799
- Type
- single nucleotide variant
- Location
- chr7:93355993 (GRCh38)
- Gene constraint
- LOEUF 0.781 · pLI 0.11 (gnomAD)
- Structure
- AlphaFold pLDDT 71.19
Similar variants
- VPS50 p.Glu700Lys Uncertain significance ★★ ⚠ same type
- VPS50 p.Asn529Tyr Likely benign ★★ same type
- VPS50 p.Asn865Ser Benign ★★ same type
- VPS50 c.2208-2A>G Likely pathogenic ★ same type
- VPS50 c.2464-1G>C Likely pathogenic ★ same type
- VPS50 p.Arg569Ter Likely pathogenic ★ same type
- VPS50 p.Gln575Ter Likely pathogenic ★ same type
- VPS50 c.102+2T>G 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/vps50-p-pro896 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown