BCAP31 p.Ile64=
c.192C>T · rs782139553 · VCV742022
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.791%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.31 | GERP -3.3, phastCons 0.58 |
| Overall | ||
| CADD | 5.746 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.791%
South Asian · 449/56,736 alleles
Filtering AF
0.731%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.707%
Overall
0.0394%
476/1,209,278 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.791% | 126 |
| Remaining individualsnot grpmax-eligible | 0.0294% | 3,399 |
| Middle Eastern | 0.023% | 4,348 |
| Admixed American | 0.00437% | 22,909 |
| African / African-American | 0.00174% | 57,331 |
| European (non-Finnish) | 0.00101% | 99,384 |
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.Ile64=
- Coding
- c.192C>T
- MANE Select
- NM_001256447
- dbSNP
- rs782139553
- Type
- single nucleotide variant
- Location
- chrX:153720873 (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-ile64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown