IL7R p.Val17=
c.51C>A · rs138981776 · VCV2965047
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, afr)
Conditions
1
immunodeficiency 104
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 |
|---|---|---|
| Pangolin | Δ0.26 | loss · gain 0.02 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -2.8 |
| Overall | ||
| CADD | 6.032 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/74,830 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00906%
Overall
0.00106%
17/1,609,418 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,345 |
| East Asian | 0.00223% | 44,864 |
| European (non-Finnish) | 0.00017% | 588,239 |
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
- IL7R
- Protein
- p.Val17=
- Coding
- c.51C>A
- MANE Select
- NM_002185
- dbSNP
- rs138981776
- Type
- single nucleotide variant
- Location
- chr5:35857028 (GRCh38)
- Gene constraint
- LOEUF 0.981 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52 · 8 PDB
Similar variants
- IL7R c.221+1G>A Pathogenic ★★★ same condition
- IL7R c.221+2T>G Pathogenic ★★★ same condition
- IL7R c.537+1G>A Pathogenic ★★★ same condition
- IL7R c.538-1G>A Pathogenic ★★★ same condition
- IL7R c.83-2A>T Pathogenic ★★★ same condition
- IL7R p.Arg206Ter Pathogenic ★★★ same condition
- IL7R p.Cys118Tyr Pathogenic ★★★ same condition
- IL7R p.Gln89Ter Likely pathogenic ★★★ 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/il7r-p-val17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown