BEST1 p.Arg13=
c.39C>T · rs1940694228 · VCV2789311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00266%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.16 | GERP -0.97, phastCons 0.007 |
| Overall | ||
| CADD | 13.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00266%
African / African-American · 2/75,060 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000205%
3/1,461,388 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00266% | 37,530 |
| East Asian | 0.00223% | 44,880 |
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
- BEST1
- Protein
- p.Arg13=
- Coding
- c.39C>T
- MANE Select
- NM_004183
- dbSNP
- rs1940694228
- Type
- single nucleotide variant
- Location
- chr11:61951845 (GRCh38)
- Gene constraint
- LOEUF 1.28 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.46 · 19 PDB
- Residue 13
- a UniProt-annotated variant site (in vmd2)
Similar variants
- BEST1 p.Arg13Cys Pathogenic/Likely pathogenic ★★ ⚠ same residue
- BEST1 p.Arg13Gly Pathogenic/Likely pathogenic ★★ ⚠ same residue
- BEST1 p.Arg13His Pathogenic/Likely pathogenic ★★ ⚠ same residue
- BEST1 p.Arg13Pro Likely pathogenic ★ same residue
- BEST1 c.1100+1G>C Pathogenic/Likely pathogenic ★★ same type
- BEST1 c.1101-1G>C Likely pathogenic ★★ same type
- BEST1 c.636+1G>A Pathogenic ★★ same type
- BEST1 c.867+97G>A Pathogenic/Likely pathogenic ★★ 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/best1-p-arg13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown