EFNA5 p.Val34=
c.102C>T · VCV4247124
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.133%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.4 | GERP -0.28, phastCons 1 |
| Overall | ||
| CADD | 13.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.133%
East Asian · 56/42,134 alleles
Filtering AF
0.105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0951%
Overall
0.00819%
129/1,574,448 alleles · rare
exomes 116/1,422,140 · genomes 13/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.133% | 752 |
| Remaining individualsnot grpmax-eligible | 0.046% | 2,176 |
| South Asian | 0.0186% | 5,373 |
| Admixed American | 0.00358% | 27,958 |
| European (non-Finnish) | 0.00233% | 42,920 |
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
- EFNA5
- Protein
- p.Val34=
- Coding
- c.102C>T
- MANE Select
- NM_001962
- Type
- single nucleotide variant
- Location
- chr5:107670512 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 79.44 · 6 PDB
- Residue 34
- a β-strand; the ephrin rbd domain
Similar variants
- EFNA5 p.Arg200His Uncertain significance ★ ⚠ same type
- EFNA5 p.Asp145His Uncertain significance ★ ⚠ same type
- EFNA5 p.Asp190Ala Uncertain significance ★ same type
- EFNA5 p.Cys164Tyr Uncertain significance ★ ⚠ same type
- EFNA5 p.Gly201Asp Uncertain significance ★ ⚠ same type
- EFNA5 p.His106Tyr Uncertain significance ★ ⚠ same type
- EFNA5 p.His171Arg Uncertain significance ★ ⚠ same type
- EFNA5 p.Leu14His 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/efna5-p-val34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown