BCAP31 c.92+293C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.7%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +293 | deep intronic (+293 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -2.8, phastCons 0.001 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 2.395 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.7%
European (non-Finnish) · 1,948/52,660 alleles
Filtering AF
3.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.51%
Overall
2.25%
2,481/110,184 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 3.7% | 27 |
| Finnishnot grpmax-eligible | 3.54% | 28 |
| Ashkenazi Jewishnot grpmax-eligible | 1.86% | 54 |
| Remaining individualsnot grpmax-eligible | 1.46% | 68 |
| South Asian | 0.974% | 103 |
| Middle Eastern | 0.917% | 109 |
| Admixed American | 0.863% | 116 |
| African / African-American | 0.444% | 225 |
| Amishnot grpmax-eligible | 0.148% | 677 |
| East Asian | 0.0572% | 1,749 |
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
- BCAP31
- Coding
- c.92+293C>T
- MANE Select
- NM_001256447
- dbSNP
- rs146728218
- Type
- single nucleotide variant
- Location
- chrX:153722860 (GRCh38)
- Structure
- AlphaFold pLDDT 84.74 · 3 PDB
Similar variants
- BCAP31 p.Arg118Cys Uncertain significance ★★ ⚠ same type
- BCAP31 p.Glu245Lys Uncertain significance ★★ ⚠ same type
- BCAP31 p.Gly165Arg Uncertain significance ★★ ⚠ same type
- BCAP31 p.Gly239Asp Uncertain significance ★★ ⚠ same type
- BCAP31 p.Ile56Val Uncertain significance ★★ ⚠ same type
- BCAP31 p.Leu226Val Uncertain significance ★★ ⚠ same type
- BCAP31 p.Leu40Pro Uncertain significance ★★ ⚠ same type
- BCAP31 p.Lys30Arg 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/bcap31-c-92-plus-293c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown