BTN2A2 p.Ser466=
c.1398G>A · rs1614887 · VCV3059725
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 87.3%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
BTN2A2-related disorder
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 -14 | GERP -3.7 |
| Overall | ||
| CADD | 0.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
87.3%
African / African-American · 65,415/74,952 alleles
Filtering AF
86.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 86.5%
Overall
54.8%
884,984/1,613,786 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 87.3% | 1 |
| Amishnot grpmax-eligible | 56.6% | 2 |
| European (non-Finnish) | 54.5% | 2 |
| Finnishnot grpmax-eligible | 54.4% | 2 |
| Remaining individualsnot grpmax-eligible | 54% | 2 |
| Middle Eastern | 52.5% | 2 |
| Admixed American | 51.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 48.6% | 2 |
| South Asian | 47.8% | 2 |
| East Asian | 33.4% | 3 |
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
- BTN2A2
- Protein
- p.Ser466=
- Coding
- c.1398G>A
- MANE Select
- NM_006995
- dbSNP
- rs1614887
- Type
- single nucleotide variant
- Location
- chr6:26392793 (GRCh38)
- Gene constraint
- LOEUF 1.093 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.50 · 1 PDB
- Residue 466
- a β-strand; the b30.2/spry domain
Disease context
BTN2A2-related disorder
Similar variants
- BTN2A2 c.443-8C>G Likely benign same condition
- BTN2A2 c.932-3C>T Likely benign same condition
- BTN2A2 c.980-88G>C Benign same condition
- BTN2A2 p.Ala192Ser Likely benign same condition
- BTN2A2 p.Ala336Thr Benign same condition
- BTN2A2 p.Asn118= Likely benign same condition
- BTN2A2 p.Gly203Ser Benign ⚠ same condition
- BTN2A2 p.Leu19= Benign same condition
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/btn2a2-p-ser466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown