BIRC6 p.Arg2090=
c.6270G>A · rs139069401 · VCV3040959
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.151%, afr)
Conditions
1
BIRC6-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 2.3 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 7.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.151%
African / African-American · 113/75,014 alleles
Filtering AF
0.128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.12%
Overall
0.00991%
160/1,613,898 alleles · rare
exomes 71/1,461,642 · genomes 89/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.151% | 664 |
| Admixed American | 0.0533% | 1,876 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| South Asian | 0.00329% | 30,360 |
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
- BIRC6
- Protein
- p.Arg2090=
- Coding
- c.6270G>A
- MANE Select
- NM_016252
- dbSNP
- rs139069401
- Type
- single nucleotide variant
- Location
- chr2:32469537 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Residue 2090
- a β-strand
Disease context
BIRC6-related disorder
Similar variants
- BIRC6 p.Gln853Arg Uncertain significance ★★ ⚠ same condition
- BIRC6 p.Glu4506Asp Uncertain significance ★★ ⚠ same condition
- BIRC6 p.Arg1075Gln Uncertain significance ★ ⚠ same condition
- BIRC6 p.Asp386Glu Uncertain significance ★ same condition
- BIRC6 p.Asp673His Uncertain significance ★ same condition
- BIRC6 p.Ser1258Ala Uncertain significance ★ ⚠ same condition
- BIRC6 p.Ser3427Phe Uncertain significance ★ same condition
- BIRC6 p.Asp3819Tyr Uncertain significance 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/birc6-p-arg2090 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown