WDR11 c.1663+19A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.2%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.52 | GERP -3.4 |
| Non-coding constraint | Z 1.41 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 0.975 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.2%
African / African-American · 149/74,426 alleles
Filtering AF
0.174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.0103%
163/1,583,674 alleles · rare
exomes 82/1,431,350 · genomes 81/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.2% | 500 |
| Remaining individualsnot grpmax-eligible | 0.013% | 7,681 |
| Admixed American | 0.01% | 9,983 |
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
- WDR11
- Coding
- c.1663+19A>C
- MANE Select
- NM_018117
- dbSNP
- rs185318998
- Type
- single nucleotide variant
- Location
- chr10:120878478 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.75 · 4 PDB
Similar variants
- WDR11 p.Gln419Ter Pathogenic ★★ same type
- WDR11 p.Ala1076Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala1203Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala26Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala954Val Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala974Val Uncertain significance ★★ ⚠ same type
- WDR11 p.Arg1185Trp Uncertain significance ★★ ⚠ same type
- WDR11 p.Arg471Cys 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/wdr11-c-1663-plus-19a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown