IL15 p.Cys136=
c.408T>C · rs145684493 · VCV790554
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.14%, 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 0.82 | GERP -1.8, phastCons 1 |
| Overall | ||
| CADD | 7.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.14%
African / African-American · 105/74,992 alleles
Filtering AF
0.118%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.11%
Overall
0.00918%
148/1,612,676 alleles · rare
exomes 88/1,460,336 · genomes 60/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.14% | 714 |
| Admixed American | 0.0117% | 8,548 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,489 |
| European (non-Finnish) | 0.00263% | 38,048 |
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
- IL15
- Protein
- p.Cys136=
- Coding
- c.408T>C
- MANE Select
- NM_000585
- dbSNP
- rs145684493
- Type
- single nucleotide variant
- Location
- chr4:141732767 (GRCh38)
- Gene constraint
- LOEUF 1.736 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.73 · 4 PDB
- Residue 136
- an α-helix; a disulfide bond
Similar variants
- IL15 p.Leu117= Benign ★★ same type
- IL15 p.Ala29Gly Uncertain significance ★ ⚠ same type
- IL15 p.Asp78Glu Uncertain significance ★ ⚠ same type
- IL15 p.Glu146Gln Uncertain significance ★ ⚠ same type
- IL15 p.His32Arg Uncertain significance ★ ⚠ same type
- IL15 p.His80Tyr Uncertain significance ★ ⚠ same type
- IL15 p.Ile144Phe Uncertain significance ★ ⚠ same type
- IL15 p.Leu73Ser 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/il15-p-cys136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown