EFNB1 p.Gln6=
c.18G>A · rs776263722 · VCV3030540
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.277%, sas)
Conditions
1
EFNB1-related disorder
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 4.2 | GERP -0.66, phastCons 1 |
| Overall | ||
| CADD | 10.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.277%
South Asian · 150/54,059 alleles
Filtering AF
0.241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.0134%
159/1,190,625 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.277% | 360 |
| Middle Eastern | 0.0232% | 4,314 |
| Remaining individualsnot grpmax-eligible | 0.015% | 6,688 |
| Admixed American | 0.00232% | 43,051 |
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
- EFNB1
- Protein
- p.Gln6=
- Coding
- c.18G>A
- MANE Select
- NM_004429
- dbSNP
- rs776263722
- Type
- single nucleotide variant
- Location
- chrX:68829794 (GRCh38)
- Structure
- AlphaFold pLDDT 71.68 · 1 PDB
Disease context
EFNB1-related disorder
Similar variants
- EFNB1 p.Gly151Ser Pathogenic ★★ same condition
- EFNB1 p.Trp12Ter Pathogenic/Likely pathogenic ★★ same condition
- EFNB1 p.Leu98Ser Likely pathogenic ★ same condition
- EFNB1 p.Lys59Asn Likely pathogenic ★ same condition
- EFNB1 p.Lys59Glu Likely pathogenic ★ ⚠ same condition
- EFNB1 p.Val164Ile Uncertain significance ★ ⚠ same condition
- EFNB1 p.Arg109His Uncertain significance ⚠ same condition
- EFNB1 c.-6G>A Likely benign same condition
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/efnb1-p-gln6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown