BNC2 p.Arg706=
c.2116A>C · rs781317873 · VCV2104303
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.37 | GERP -3.4, phastCons 0.11 |
| Overall | ||
| CADD | 6.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BNC2
- Protein
- p.Arg706=
- Coding
- c.2116A>C
- MANE Select
- NM_017637
- dbSNP
- rs781317873
- Type
- single nucleotide variant
- Location
- chr9:16436078 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
- Residue 706
- 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-arg706 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown