Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 39.4%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
cataract 33
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 |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -3.5 |
| Overall | ||
| CADD | 3.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
39.4%
East Asian · 17,659/44,866 alleles
Filtering AF
38.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 38.7%
Overall
25.7%
415,318/1,613,960 alleles · common
exomes 372,396/1,461,856 · genomes 42,922/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 39.4% | 3 |
| South Asian | 35.4% | 3 |
| African / African-American | 34% | 3 |
| Admixed American | 33% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 28.7% | 3 |
| Middle Eastern | 27.3% | 4 |
| Remaining individualsnot grpmax-eligible | 27.1% | 4 |
| European (non-Finnish) | 23.6% | 4 |
| Finnishnot grpmax-eligible | 22.1% | 5 |
| Amishnot grpmax-eligible | 14.6% | 7 |
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
- BFSP1
- Protein
- p.Ala500=
- Coding
- c.1500G>A
- MANE Select
- NM_001195
- dbSNP
- rs6136118
- Type
- single nucleotide variant
- Location
- chr20:17494572 (GRCh38)
- Gene constraint
- LOEUF 1.371 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.66
- Residue 500
- the 'tail' region
Similar variants
- BFSP1 p.Ala643Thr Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Arg560Cys Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Arg69Trp Uncertain significance ★★ same condition
- BFSP1 p.Asp19Asn Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Gln294Arg Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Gly46Trp Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Ile271Thr Uncertain significance ★★ ⚠ same condition
- BFSP1 p.Leu68Phe 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/bfsp1-p-ala500 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown