WDR11 c.1663+102T>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 46.7%, amr) — 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 | ||
| Splice region | donor +102 | deep intronic (+102 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -2.6, phastCons 0.12 |
| Non-coding constraint | Z 1.41 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 5.117 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
46.7%
Admixed American · 21,843/46,754 alleles
Filtering AF
46.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 46%
Overall
33.7%
298,613/886,614 alleles · common
exomes 251,424/734,656 · genomes 47,189/151,958 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 46.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 40.2% | 2 |
| East Asian | 38.5% | 3 |
| Amishnot grpmax-eligible | 38% | 3 |
| Remaining individualsnot grpmax-eligible | 34.2% | 3 |
| European (non-Finnish) | 33.9% | 3 |
| Middle Eastern | 32.5% | 3 |
| South Asian | 32.3% | 3 |
| Finnishnot grpmax-eligible | 29% | 3 |
| African / African-American | 21% | 5 |
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+102T>A
- MANE Select
- NM_018117
- dbSNP
- rs1992274
- Type
- single nucleotide variant
- Location
- chr10:120878561 (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-102t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown