CELF2 c.976+4A>T
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
CELF2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.83 | donor gain · deltas |
| Pangolin | Δ0.79 | loss · gain 0.64 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.8, phastCons 1 |
| Non-coding constraint | Z 2.46 | 1 kb window · o/e 0.77 · regional · uncalibrated |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CELF2
- Coding
- c.976+4A>T
- MANE Select
- NM_001326342
- dbSNP
- rs2549302443
- Type
- single nucleotide variant
- Location
- chr10:11288556 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.26 · 7 PDB
Disease context
CELF2-related disorder
Similar variants
- CELF2 p.Met1Lys Uncertain significance ★ same condition
- CELF2 c.977-2A>T Likely pathogenic same condition
- CELF2 c.1097-6G>T Likely benign same condition
- CELF2 c.16+5G>A Likely benign same condition
- CELF2 p.Leu17Ser Likely benign same condition
- CELF2 p.Leu4Val Likely benign same condition
- CELF2 p.Arg506Cys Pathogenic/Likely pathogenic ★★ same type
- CELF2 p.Arg513His Likely pathogenic ★★ 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/celf2-c-976-plus-4a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown