Computational evidence
| Protein change | ||
| AlphaMissense | 0.0573 | likely benign |
|---|---|---|
| REVEL | 0.274 | benign-leaning |
| SaProt | LLR -5.04 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.32 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 0.6, phastCons 1 |
| Regional constraint | o/e 0.87 | unconstrained · MANE · 35 kb · p 9.6e-05 · regional, not allelic |
| Overall | ||
| CADD | 18.02 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Finnishnot grpmax-eligible | 99.9% | 1 |
| African / African-American | 99.9% | 1 |
| Admixed American | 99.5% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 99.5% | 1 |
| Remaining individualsnot grpmax-eligible | 99.4% | 1 |
| European (non-Finnish) | 99.3% | 1 |
| South Asian | 99% | 1 |
| Middle Eastern | 98.6% | 1 |
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
- Protein
- p.Ser70Asn
- Coding
- c.209G>A
- MANE Select
- NM_031885
- dbSNP
- rs4784677
- Type
- single nucleotide variant
- Location
- chr16:56514589 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
- Residue 70
- a UniProt-annotated variant site (in)
Similar variants
- BBS2 p.Ser70= Benign ★ same residue
- BBS2 c.118-1G>T Likely pathogenic ★★ same condition
- BBS2 c.118-2A>C Likely pathogenic ★★ same condition
- BBS2 c.118-2A>G Likely pathogenic ★★ same condition
- BBS2 c.1225+2T>C Likely pathogenic ★★ same condition
- BBS2 c.1225+2T>G Likely pathogenic ★★ same condition
- BBS2 c.1397+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BBS2 c.1397+2T>C 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-p-ser70asn (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown