BBS10 p.Ser558=
c.1674T>G · rs769632511 · VCV434483
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, nfe)
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 4 | GERP 1.6, phastCons 0.77 |
| Overall | ||
| CADD | 1.567 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,179,882 alleles
Filtering AF
0.000542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000428%
Overall
0.000821%
12/1,461,510 alleles · very rare
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
- BBS10
- Protein
- p.Ser558=
- Coding
- c.1674T>G
- MANE Select
- NM_024685
- dbSNP
- rs769632511
- Type
- single nucleotide variant
- Location
- chr12:76346311 (GRCh38)
- Gene constraint
- LOEUF 1.418 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.26
Similar variants
- BBS10 p.Ser558Tyr Uncertain significance ⚠ same residue
- BBS10 p.Ser558_Tyr559insTer Pathogenic ★★ same residue
- BBS10 p.Ser558del Uncertain significance ★ same residue
- BBS10 c.197+1G>T Pathogenic/Likely pathogenic ★★ same type
- BBS10 p.Arg256Ter Pathogenic ★★ same type
- BBS10 p.Arg49Leu Likely pathogenic ★★ ⚠ same type
- BBS10 p.Arg49Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- BBS10 p.Cys28Ter Pathogenic/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/bbs10-p-ser558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown