BEST3 p.Val49=
c.147A>G · rs775429 · VCV1272982
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
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 -0.081 | GERP -1, phastCons 0.54 |
| Overall | ||
| CADD | 7.592 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,042/44,042 alleles
Filtering AF
99.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.8%
Overall
99.6%
1,580,445/1,587,198 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| Finnishnot grpmax-eligible | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| South Asian | 100% | 1 |
| European (non-Finnish) | 100% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 99.9% | 1 |
| Middle Eastern | 99.7% | 1 |
| Remaining individualsnot grpmax-eligible | 99.5% | 1 |
| Admixed American | 99.4% | 1 |
| African / African-American | 92.2% | 1 |
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
- BEST3
- Protein
- p.Val49=
- Coding
- c.147A>G
- MANE Select
- NM_032735
- dbSNP
- rs775429
- Type
- single nucleotide variant
- Location
- chr12:69697652 (GRCh38)
- Gene constraint
- LOEUF 1.275 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.66
Similar variants
- BEST3 p.Pro383Leu Benign ★★ same type
- BEST3 p.Ala351Gly Uncertain significance ★ ⚠ same type
- BEST3 p.Arg141Ser Uncertain significance ★ ⚠ same type
- BEST3 p.Arg196Gln Uncertain significance ★ ⚠ same type
- BEST3 p.Arg196Trp Uncertain significance ★ ⚠ same type
- BEST3 p.Arg202Ile Uncertain significance ★ ⚠ same type
- BEST3 p.Arg216Gly Uncertain significance ★ ⚠ same type
- BEST3 p.Arg218Cys 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/best3-p-val49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown