EBP c.338+10del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.19 | GERP -1.5, phastCons 0.86 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- EBP
- Coding
- c.338+10del
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs2519111118
- Type
- Deletion
- Location
- chrX:48527033 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
Similar variants
- EBP p.Ala54fs Likely pathogenic ★ same type
- EBP p.Asp162fs Pathogenic ★ same type
- EBP p.Phe36fs Pathogenic ★ same type
- EBP p.Ser98fs Pathogenic ★ same type
- EBP p.Thr168fs Likely pathogenic ★ same type
- EBP p.Val43fs Pathogenic ★ same type
- EBP p.Ala225fs Uncertain significance ★ same type
- EBP p.Ser37del 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/ebp-c-338-plus-10del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown