B9D1 p.Ala151=
c.453T>C · VCV3755024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Conditions
2
Joubert syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.21 | GERP -2.9, phastCons 0.003 |
| Overall | ||
| CADD | 6.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,084 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000372%
6/1,614,112 alleles · very rare
exomes 6/1,461,846 · genomes 0/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,361 |
| European (non-Finnish) | 0.000254% | 393,331 |
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
- B9D1
- Protein
- p.Ala151=
- Coding
- c.453T>C
- MANE Select
- NM_015681
- Type
- single nucleotide variant
- Location
- chr17:19343809 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.05
Similar variants
- B9D1 c.341+2T>C Pathogenic/Likely pathogenic ★★ same condition
- B9D1 p.Arg114Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- B9D1 p.Arg156Trp Pathogenic/Likely pathogenic ★★ same condition
- B9D1 c.404+5G>C Uncertain significance ★★ same condition
- B9D1 p.Ala44Val Uncertain significance ★★ ⚠ same condition
- B9D1 p.Arg101Gln Uncertain significance ★★ same condition
- B9D1 p.Arg140Gln Uncertain significance ★★ ⚠ same condition
- B9D1 p.Arg162His Uncertain significance ★★ ⚠ 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/b9d1-p-ala151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown