BFSP1 c.2+231C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.31%, afr) — 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 +231 | deep intronic (+231 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -1.1, phastCons 0.99 |
| Non-coding constraint | Z 1.57 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 8.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.31%
African / African-American · 2,619/41,504 alleles
Filtering AF
6.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.03%
Overall
1.82%
2,765/152,216 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.31% | 16 |
| Remaining individualsnot grpmax-eligible | 1.47% | 68 |
| Middle Eastern | 1.02% | 98 |
| Admixed American | 0.608% | 164 |
| Ashkenazi Jewishnot grpmax-eligible | 0.231% | 433 |
| South Asian | 0.0829% | 1,206 |
| European (non-Finnish) | 0.0103% | 9,715 |
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
- Coding
- c.2+231C>T
- MANE Select
- NM_001195 · reported on NM_001161705
- dbSNP
- rs11905929
- Type
- single nucleotide variant
- Location
- chr20:17558457 (GRCh38)
- Gene constraint
- LOEUF 1.371 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.66
Similar variants
- BFSP1 p.Ala643Thr Uncertain significance ★★ ⚠ same type
- BFSP1 p.Arg560Cys Uncertain significance ★★ ⚠ same type
- BFSP1 p.Arg69Trp Uncertain significance ★★ ⚠ same type
- BFSP1 p.Asp19Asn Uncertain significance ★★ ⚠ same type
- BFSP1 p.Gln294Arg Uncertain significance ★★ ⚠ same type
- BFSP1 p.Glu93Asp Uncertain significance ★★ ⚠ same type
- BFSP1 p.Gly46Trp Uncertain significance ★★ ⚠ same type
- BFSP1 p.Ile271Thr Uncertain significance ★★ ⚠ 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/bfsp1-c-2-plus-231c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown