BGN p.His68=
c.204C>T · rs1556992685 · VCV2995179
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000112%, nfe)
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 1.1 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 9.125 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000112%
European (non-Finnish) · 1/895,177 alleles
Overall
8.27e-05%
1/1,209,716 alleles · very rare
exomes 1/1,095,560 · genomes 0/114,156 · joint denominator
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
- BGN
- Protein
- p.His68=
- Coding
- c.204C>T
- MANE Select
- NM_001711
- dbSNP
- rs1556992685
- Type
- single nucleotide variant
- Location
- chrX:153504835 (GRCh38)
- Structure
- AlphaFold pLDDT 85.72
Similar variants
- BGN c.770+1G>A Likely pathogenic ★★ same type
- BGN p.Gln75Ter Pathogenic/Likely pathogenic ★★ same type
- BGN p.Trp25Ter Likely pathogenic ★★ same type
- BGN c.909+4A>G Uncertain significance ★★ same type
- BGN p.Ala330Asp Uncertain significance ★★ ⚠ same type
- BGN p.Ala330Pro Uncertain significance ★★ ⚠ same type
- BGN p.Ala41Ser Uncertain significance ★★ ⚠ same type
- BGN p.Ala44Thr 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/bgn-p-his68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown