BCAP31 p.Leu103=
c.309C>G · rs142876751 · VCV2887238
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0455%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 16.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0455%
African / African-American · 26/57,129 alleles
Filtering AF
0.0318%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0273%
Overall
0.00231%
28/1,209,787 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0455% | 2,197 |
| Admixed American | 0.00219% | 45,718 |
| Finnishnot grpmax-eligible | 0.00215% | 46,540 |
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
- Protein
- p.Leu103=
- Coding
- c.309C>G
- MANE Select
- NM_001256447
- dbSNP
- rs142876751
- Type
- single nucleotide variant
- Location
- chrX:153715574 (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-p-leu103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown