WNT9B p.Val282=
c.846G>C · rs754474 · VCV1598961
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 27.5%, afr) — 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. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.84 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 6.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
27.5%
African / African-American · 20,639/75,022 alleles
Filtering AF
27.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 27.1%
Overall
2.75%
44,433/1,613,578 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 27.5% | 4 |
| Amishnot grpmax-eligible | 6.81% | 15 |
| Middle Eastern | 3.61% | 28 |
| Remaining individualsnot grpmax-eligible | 3.32% | 30 |
| Admixed American | 2.85% | 35 |
| Ashkenazi Jewishnot grpmax-eligible | 2.63% | 38 |
| Finnishnot grpmax-eligible | 1.53% | 65 |
| European (non-Finnish) | 1.5% | 67 |
| South Asian | 0.347% | 288 |
| East Asian | 0.00891% | 11,218 |
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.Val282=
- Coding
- c.846G>C
- MANE Select
- NM_003396
- dbSNP
- rs754474
- Type
- single nucleotide variant
- Location
- chr17:46876490 (GRCh38)
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-val282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown