EPHB4 c.1870+9C>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -2.1 |
| Overall | ||
| CADD | 0.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0988%
South Asian · 90/91,064 alleles
Filtering AF
0.0823%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0762%
Overall
0.00589%
95/1,613,418 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0988% | 1,012 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,251 |
| European (non-Finnish) | 0.000254% | 393,326 |
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
- EPHB4
- Coding
- c.1870+9C>A
- MANE Select
- NM_004444
- dbSNP
- rs201075640
- Type
- single nucleotide variant
- Location
- chr7:100813086 (GRCh38)
- Gene constraint
- LOEUF 0.645 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.46 · 23 PDB
Similar variants
- EPHB4 c.1691+1G>A Pathogenic/Likely pathogenic ★★ same type
- EPHB4 c.2484+1G>A Pathogenic/Likely pathogenic ★★ same type
- EPHB4 p.Arg269Ter Pathogenic/Likely pathogenic ★★ same type
- EPHB4 p.Arg365Ter Pathogenic/Likely pathogenic ★★ same type
- EPHB4 p.Arg394Ter Pathogenic ★★ same type
- EPHB4 p.Arg431Ter Pathogenic ★★ same type
- EPHB4 p.Arg739Gln Pathogenic ★★ same type
- EPHB4 p.Arg739Ter 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/ephb4-c-1870-plus-9c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown