BNC2 p.Ile221=
c.663C>T · rs149390976 · VCV2767660
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.324%, afr)
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 5.7 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 11.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.324%
African / African-American · 243/75,060 alleles
Filtering AF
0.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.277%
Overall
0.0176%
284/1,614,092 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.324% | 309 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| Admixed American | 0.0217% | 4,616 |
| South Asian | 0.0022% | 45,532 |
| European (non-Finnish) | 0.000678% | 147,495 |
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
- BNC2
- Protein
- p.Ile221=
- Coding
- c.663C>T
- MANE Select
- NM_017637
- dbSNP
- rs149390976
- Type
- single nucleotide variant
- Location
- chr9:16552536 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
Similar variants
- BNC2 p.Ile221Val Uncertain significance ★ ⚠ same residue
- BNC2 p.Ala386Val Uncertain significance ★★ ⚠ same type
- BNC2 p.Arg536Gln Uncertain significance ★★ ⚠ same type
- BNC2 p.Arg875His Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn1032Ser Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn1088Asp Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn668Ser Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn795Ser 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/bnc2-p-ile221 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown