WNT9B p.Pro45=
c.135G>A · rs372193837 · VCV1632396
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.02%, sas)
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 -9.6 | GERP -8 |
| Overall | ||
| CADD | 0.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.02%
South Asian · 907/89,232 alleles
Filtering AF
0.962%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.94%
Overall
0.0614%
982/1,600,106 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.02% | 98 |
| Remaining individualsnot grpmax-eligible | 0.076% | 1,315 |
| Middle Eastern | 0.0688% | 1,453 |
| Admixed American | 0.00849% | 11,784 |
| East Asian | 0.00674% | 14,841 |
| African / African-American | 0.00134% | 74,774 |
| European (non-Finnish) | 0.00128% | 78,119 |
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
- WNT9B
- Protein
- p.Pro45=
- Coding
- c.135G>A
- MANE Select
- NM_003396
- dbSNP
- rs372193837
- Type
- single nucleotide variant
- Location
- chr17:46872574 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50
Similar variants
- WNT9B p.Arg325His Uncertain significance ★ ⚠ same type
- WNT9B c.600+8T>G Likely benign ★ same type
- WNT9B p.Asp191= Benign ★ same type
- WNT9B p.Arg97His Likely benign 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/wnt9b-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown