BCAP31 c.341+87del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 15.7%, 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 +87 | deep intronic (+87 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.71 | GERP -1.2 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 1.769 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.7%
African / African-American · 8,592/54,844 alleles
Filtering AF
15.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.3%
Overall
0.88%
9,835/1,117,931 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 15.7% | 6 |
| Admixed American | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 1.18% | 85 |
| Middle Eastern | 0.617% | 162 |
| South Asian | 0.0498% | 2,007 |
| European (non-Finnish) | 0.0156% | 6,410 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00492% | 20,312 |
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.341+87del
- MANE Select
- NM_001256447
- dbSNP
- rs200005341
- Type
- Deletion
- Location
- chrX:153715455 (GRCh38)
- Structure
- AlphaFold pLDDT 84.74 · 3 PDB
Similar variants
- BCAP31 p.Ala99fs Pathogenic ★ same type
- BCAP31 p.Gly165fs Likely pathogenic ★ same type
- BCAP31 c.477+8del Uncertain significance ★ same type
- BCAP31 c.194-18del Likely benign ★ same type
- BCAP31 c.194-315del Benign ★ same type
- BCAP31 c.703-135del Benign ★ same type
- BCAP31 c.-12_-10del Likely benign 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-341-plus-87del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown