ELN c.1096+4A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 | Δ0.54 | donor gain · deltas |
| Pangolin | Δ0.29 | loss · gain 0.09 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 4.5, phastCons 0.79 |
| Non-coding constraint | Z 1.30 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 26.0 | 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
- ELN
- Coding
- c.1096+4A>G
- MANE Select
- NM_000501
- Type
- single nucleotide variant
- Location
- chr7:74053313 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
Similar variants
- ELN c.134-1G>A Likely pathogenic ★★ same type
- ELN c.377-2A>G Pathogenic/Likely pathogenic ★★ same type
- ELN c.643+1G>A Pathogenic/Likely pathogenic ★★ same type
- ELN c.643+1G>C Likely pathogenic ★★ same type
- ELN c.686-2A>G Likely pathogenic ★★ same type
- ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same type
- ELN c.800-2A>G Pathogenic ★★ same type
- ELN c.800-3C>G 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/eln-c-1096-plus-4a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown