Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.14%, 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 -0.071 | GERP -2.5 |
| Overall | ||
| CADD | 4.164 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.14%
African / African-American · 3,105/75,022 alleles
Filtering AF
4.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.97%
Overall
0.217%
3,500/1,614,138 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.14% | 24 |
| Remaining individualsnot grpmax-eligible | 0.283% | 353 |
| Admixed American | 0.235% | 426 |
| Middle Eastern | 0.165% | 606 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00517% | 19,345 |
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
- BIRC3
- Protein
- p.Lys87=
- Coding
- c.261A>G
- MANE Select
- NM_001165
- dbSNP
- rs7930386
- Type
- single nucleotide variant
- Location
- chr11:102324770 (GRCh38)
- Gene constraint
- LOEUF 0.543 · pLI 0.81 (gnomAD)
- Structure
- AlphaFold pLDDT 75.13 · 6 PDB
- Residue 87
- an α-helix
Similar variants
- BIRC3 p.Arg401Lys Likely benign ★★ same type
- BIRC3 p.Arg555= Benign ★★ same type
- BIRC3 p.Asp530His Likely pathogenic ★ ⚠ same type
- BIRC3 p.Cys557Ter Likely pathogenic ★ same type
- BIRC3 p.Cys588Tyr Likely pathogenic ★ same type
- BIRC3 p.His312Tyr Likely pathogenic ★ same type
- BIRC3 p.Ter605Arg Likely pathogenic ★ same type
- BIRC3 p.Thr35Ala 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/birc3-p-lys87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown