BGN p.Ser103=
c.309C>T · rs1469006247 · VCV2983148
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, mid)
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 -13 | GERP -3.8 |
| Overall | ||
| CADD | 0.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
Middle Eastern · 1/4,351 alleles
Filtering AF
0.000565%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000412%
Overall
0.000991%
12/1,210,664 alleles · ultra-rare
exomes 12/1,097,082 · genomes 0/113,582 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.023% | 4,351 |
| African / African-American | 0.00173% | 57,720 |
| European (non-Finnish) | 0.00112% | 89,467 |
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.Ser103=
- Coding
- c.309C>T
- MANE Select
- NM_001711
- dbSNP
- rs1469006247
- Type
- single nucleotide variant
- Location
- chrX:153505308 (GRCh38)
- Structure
- AlphaFold pLDDT 85.72
Similar variants
- BGN p.Ser103Pro Uncertain significance ★ ⚠ same residue
- 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
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-ser103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown