EPHB2 p.Gly515=
c.1545T>C · rs309472 · VCV1174736
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
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 0.61 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 11.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,876/44,876 alleles
Filtering AF
99.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.2%
Overall
99.5%
1,605,603/1,614,264 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Middle Eastern | 100% | 1 |
| South Asian | 99.9% | 1 |
| African / African-American | 99.9% | 1 |
| Finnishnot grpmax-eligible | 99.8% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 99.7% | 1 |
| Admixed American | 99.7% | 1 |
| Remaining individualsnot grpmax-eligible | 99.6% | 1 |
| European (non-Finnish) | 99.3% | 1 |
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.Gly515=
- Coding
- c.1545T>C
- MANE Select
- NM_017449
- dbSNP
- rs309472
- Type
- single nucleotide variant
- Location
- chr1:22893000 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
- Residue 515
- the fibronectin type-iii 2 domain
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-gly515 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown