BCAP31 p.Ala14=
c.42G>A · rs782120731 · VCV2075685
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00175%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -3.1 |
| Overall | ||
| CADD | 6.718 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00175%
African / African-American · 1/57,103 alleles
Filtering AF
0.00066%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000482%
Overall
0.000993%
12/1,208,732 alleles · very rare
exomes 7/1,097,286 · genomes 5/111,446 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00175% | 57,103 |
| European (non-Finnish) | 0.00123% | 81,317 |
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.Ala14=
- Coding
- c.42G>A
- MANE Select
- NM_001256447
- dbSNP
- rs782120731
- Type
- single nucleotide variant
- Location
- chrX:153723203 (GRCh38)
- Structure
- AlphaFold pLDDT 84.74 · 3 PDB
Similar variants
- BCAP31 p.Ala14Gly Uncertain significance ★ ⚠ same residue
- BCAP31 p.Ala14Val Uncertain significance ★ ⚠ same residue
- 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
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-ala14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown