BCAN p.Val651=
c.1953C>T · rs548144047 · VCV733328
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.282%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.25 | GERP 0.023, phastCons 0.19 |
| Overall | ||
| CADD | 9.259 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.282%
South Asian · 169/59,942 alleles
Filtering AF
0.247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.234%
Overall
0.012%
175/1,459,908 alleles · rare
exomes 161/1,307,702 · genomes 14/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.282% | 355 |
| Remaining individualsnot grpmax-eligible | 0.00898% | 11,138 |
| European (non-Finnish) | 8.97e-05% | 1,115,053 |
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
- BCAN
- Protein
- p.Val651=
- Coding
- c.1953C>T
- MANE Select
- NM_021948
- dbSNP
- rs548144047
- Type
- single nucleotide variant
- Location
- chr1:156656292 (GRCh38)
- Gene constraint
- LOEUF 0.695 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06
- Residue 651
- the egf-like domain
Similar variants
- BCAN p.Arg105Gly Benign ★★ same type
- BCAN p.Ala10Pro Uncertain significance ★ ⚠ same type
- BCAN p.Ala112Thr Uncertain significance ★ ⚠ same type
- BCAN p.Ala166Val Uncertain significance ★ ⚠ same type
- BCAN p.Ala169Thr Uncertain significance ★ ⚠ same type
- BCAN p.Ala2Thr Uncertain significance ★ ⚠ same type
- BCAN p.Ala357Thr Uncertain significance ★ ⚠ same type
- BCAN p.Ala357Val 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/bcan-p-val651 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown