BIRC3 p.Arg555=
c.1663A>C · rs57261191 · VCV730991
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.3%, 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 2.8 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 9.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.3%
African / African-American · 967/74,368 alleles
Filtering AF
1.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2%
Overall
0.0836%
1,340/1,603,642 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.3% | 77 |
| Middle Eastern | 0.331% | 302 |
| Ashkenazi Jewishnot grpmax-eligible | 0.256% | 391 |
| Remaining individualsnot grpmax-eligible | 0.174% | 576 |
| Admixed American | 0.0882% | 1,134 |
| European (non-Finnish) | 0.00976% | 10,241 |
| South Asian | 0.0057% | 17,550 |
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.Arg555=
- Coding
- c.1663A>C
- MANE Select
- NM_001165
- dbSNP
- rs57261191
- Type
- single nucleotide variant
- Location
- chr11:102336950 (GRCh38)
- Gene constraint
- LOEUF 0.543 · pLI 0.81 (gnomAD)
- Structure
- AlphaFold pLDDT 75.13 · 6 PDB
- Residue 555
- an α-helix
Similar variants
- BIRC3 p.Arg401Lys Likely benign ★★ same type
- BIRC3 p.Lys87= 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-arg555 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown