BOC p.Gln955=
c.2865G>A · rs759135103 · VCV2654038
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, afr)
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 0.48 | GERP -0.47, phastCons 0.001 |
| Overall | ||
| CADD | 0.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,930 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00174%
28/1,613,438 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,746 |
| Admixed American | 0.00667% | 14,984 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,815 |
| South Asian | 0.0011% | 91,022 |
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
- BOC
- Protein
- p.Gln955=
- Coding
- c.2865G>A
- MANE Select
- NM_001378074
- dbSNP
- rs759135103
- Type
- single nucleotide variant
- Location
- chr3:113284543 (GRCh38)
- Gene constraint
- LOEUF 0.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.98 · 3 PDB
Similar variants
- BOC p.Ala715= Benign ★★ same type
- BOC p.Lys884Asn Benign ★★ same type
- BOC p.Pro829Arg Benign ★★ same type
- BOC p.Pro913Ser Benign ★★ same type
- BOC p.Ala226Thr Uncertain significance ★ ⚠ same type
- BOC p.Ala424Thr Uncertain significance ★ ⚠ same type
- BOC p.Ala470Val Uncertain significance ★ ⚠ same type
- BOC p.Ala503Val 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/boc-p-gln955 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown