CELF2 c.16+5G>A
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.239%, afr)
Conditions
1
CELF2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +5 | donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 1.8, phastCons 0.99 |
| Non-coding constraint | Z 1.72 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 16.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.239%
African / African-American · 137/57,360 alleles
Filtering AF
0.206%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.0153%
151/984,996 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.239% | 419 |
| Admixed American | 0.0368% | 2,715 |
| Remaining individualsnot grpmax-eligible | 0.0238% | 4,201 |
| South Asian | 0.0047% | 21,276 |
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
- CELF2
- Coding
- c.16+5G>A
- MANE Select
- NM_001326342 · reported on NM_001326325
- dbSNP
- rs369822439
- Type
- single nucleotide variant
- Location
- chr10:10796908 (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.976+4A>T Uncertain significance same condition
- CELF2 c.1097-6G>T 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-16-plus-5g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown