BTN3A2 p.Ser327=
c.981G>A · rs115820857 · VCV768070
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.22%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -1.1 |
| Overall | ||
| CADD | 2.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.22%
African / African-American · 3,145/74,494 alleles
Filtering AF
4.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.05%
Overall
0.33%
5,320/1,611,670 alleles · low-frequency
exomes 3,313/1,460,900 · genomes 2,007/150,770 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.22% | 24 |
| Admixed American | 0.776% | 129 |
| Remaining individualsnot grpmax-eligible | 0.444% | 225 |
| Middle Eastern | 0.331% | 302 |
| European (non-Finnish) | 0.114% | 874 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0744% | 1,344 |
| South Asian | 0.0308% | 3,249 |
| East Asian | 0.0157% | 6,385 |
| Finnishnot grpmax-eligible | 0.0126% | 7,945 |
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
- BTN3A2
- Protein
- p.Ser327=
- Coding
- c.981G>A
- MANE Select
- NM_007047
- dbSNP
- rs115820857
- Type
- single nucleotide variant
- Location
- chr6:26374343 (GRCh38)
- Gene constraint
- LOEUF 1.043 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.23 · 18 PDB
Similar variants
- BTN3A2 p.Ser327Trp Uncertain significance ★ ⚠ same residue
- BTN3A2 p.Ala110Thr Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala182Asp Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala192Val Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala233Gly Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala245Thr Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala264Thr Uncertain significance ★ ⚠ same type
- BTN3A2 p.Ala266Val 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/btn3a2-p-ser327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown