BBS2 c.117+15C>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
Bardet-Biedl syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +15 | near-intronic (+15 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -2.9, phastCons 0.004 |
| Non-coding constraint | Z -2.54 | 1 kb window · o/e 1.19 · regional · uncalibrated |
| Overall | ||
| CADD | 6.579 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,954 alleles
Overall
0.000138%
2/1,450,762 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,954 |
| European (non-Finnish) | 8.54e-05% | 1,171,374 |
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
- BBS2
- Coding
- c.117+15C>G
- MANE Select
- NM_031885
- dbSNP
- rs765794155
- Type
- single nucleotide variant
- Location
- chr16:56519731 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
Disease context
Bardet-Biedl syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Bardet-Biedl syndrome (Orphanet):
- Inheritance
- Autosomal recessive, Oligogenic
- Onset
- Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Specific population)
Similar variants
- BBS2 c.118-1G>T Likely pathogenic ★★ same condition
- BBS2 c.118-2A>C Likely pathogenic ★★ same condition
- BBS2 c.1225+2T>C Likely pathogenic ★★ same condition
- BBS2 c.1397+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BBS2 c.1397+2T>C Likely pathogenic ★★ same condition
- BBS2 c.1398-2A>G Likely pathogenic ★★ same condition
- BBS2 c.1527+1G>A Likely pathogenic ★★ same condition
- BBS2 c.345+1G>A Likely pathogenic ★★ 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/bbs2-c-117-plus-15c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown