BNC2 p.Pro660=
c.1980C>T · rs141360036 · VCV2768109
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0387%, 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 3 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 6.651 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0387%
African / African-American · 29/74,996 alleles
Filtering AF
0.0276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0238%
Overall
0.00242%
39/1,614,074 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0387% | 2,586 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.01% | 10,001 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Pro660=
- Coding
- c.1980C>T
- MANE Select
- NM_017637
- dbSNP
- rs141360036
- Type
- single nucleotide variant
- Location
- chr9:16436214 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
- Residue 660
- the 'disordered' region
Similar variants
- 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
- BNC2 p.Asp690Glu 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-pro660 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown