EBP c.301+19C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000184%)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.039 | GERP -3.1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 3.863 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000184%
Overall
0.000184%
2/1,089,853 alleles · very rare
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
- EBP
- Coding
- c.301+19C>A
- MANE Select
- NM_001378122 · reported on NM_006579
- Type
- single nucleotide variant
- Location
- chrX:48524091 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
Similar variants
- EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same type
- EBP p.Arg110Ter Pathogenic ★★ same type
- EBP p.Arg147Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- EBP p.Arg147His Pathogenic ★★ ⚠ same type
- EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same type
- EBP p.Gly161Arg Likely pathogenic ★★ same type
- EBP p.Ser98Phe Pathogenic/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/ebp-c-301-plus-19c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown