Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.755%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 7.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.755%
African / African-American · 567/75,082 alleles
Filtering AF
0.704%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.683%
Overall
0.0397%
641/1,614,006 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.755% | 132 |
| Admixed American | 0.0683% | 1,464 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,156 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 590,030 |
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
- EPHB2
- Protein
- p.Leu219=
- Coding
- c.657G>A
- MANE Select
- NM_017449
- dbSNP
- rs1371869
- Type
- single nucleotide variant
- Location
- chr1:22784922 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
Similar variants
- EPHB2 p.Val414Ile Uncertain significance ★★ ⚠ same type
- EPHB2 c.1766-9G>T Benign/Likely benign ★★ same type
- EPHB2 p.Ala279Ser Benign ★★ same type
- EPHB2 p.Asn242= Likely benign ★★ same type
- EPHB2 p.Asp574= Benign ★★ same type
- EPHB2 p.Asp678Asn Likely benign ★★ same type
- EPHB2 p.Gln875= Benign ★★ same type
- EPHB2 p.Ser170= Benign ★★ 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/ephb2-p-leu219 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown