BBS2 c.940+91C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 12.6%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +91 | deep intronic (+91 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -0.46, phastCons 0.003 |
| Non-coding constraint | Z 1.23 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 3.622 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.6%
South Asian · 11,479/90,874 alleles
Filtering AF
12.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.4%
Overall
4.67%
75,227/1,609,478 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 12.6% | 8 |
| East Asian | 12.6% | 8 |
| Remaining individualsnot grpmax-eligible | 5.19% | 19 |
| Finnishnot grpmax-eligible | 4.58% | 22 |
| Middle Eastern | 4.1% | 24 |
| European (non-Finnish) | 4% | 25 |
| Admixed American | 3.96% | 25 |
| African / African-American | 2.4% | 42 |
| Ashkenazi Jewishnot grpmax-eligible | 1.77% | 57 |
| Amishnot grpmax-eligible | 0.768% | 130 |
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.940+91C>T
- MANE Select
- NM_031885
- dbSNP
- rs41280890
- Type
- single nucleotide variant
- Location
- chr16:56502582 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
Similar variants
- BBS2 c.118-1G>T Likely pathogenic ★★ same type
- BBS2 c.118-2A>C Likely pathogenic ★★ same type
- BBS2 c.118-2A>G Likely pathogenic ★★ same type
- BBS2 c.1225+2T>C Likely pathogenic ★★ same type
- BBS2 c.1225+2T>G Likely pathogenic ★★ same type
- BBS2 c.1397+1G>A Pathogenic/Likely pathogenic ★★ same type
- BBS2 c.1397+2T>C Likely pathogenic ★★ same type
- BBS2 c.1398-2A>G Likely pathogenic ★★ 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/bbs2-c-940-plus-91c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown