BNC2 p.Pro606=
c.1818G>A · rs142872531 · VCV2070041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0933%, 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 -2.1 | GERP -3.7 |
| Overall | ||
| CADD | 4.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0933%
African / African-American · 70/74,992 alleles
Filtering AF
0.0757%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0693%
Overall
0.00731%
118/1,613,974 alleles · ultra-rare
exomes 76/1,461,836 · genomes 42/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0933% | 1,071 |
| Admixed American | 0.0283% | 3,530 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,944 |
| East Asian | 0.00446% | 22,438 |
| European (non-Finnish) | 0.00161% | 62,106 |
| South Asian | 0.0011% | 91,064 |
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.Pro606=
- Coding
- c.1818G>A
- MANE Select
- NM_017637
- dbSNP
- rs142872531
- Type
- single nucleotide variant
- Location
- chr9:16436376 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
Similar variants
- BNC2 p.Pro606Leu Benign ★★ same residue
- BNC2 p.Pro606Ser 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
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-pro606 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown