IFNAR1 p.Val56=
c.168C>T · rs779146071 · VCV1567811
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00516%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -2.5 |
| Overall | ||
| CADD | 2.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00516%
Admixed American · 3/58,180 alleles
Filtering AF
0.00137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000906%
Overall
0.00169%
27/1,598,138 alleles · very rare
exomes 23/1,446,048 · genomes 4/152,090 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00516% | 19,393 |
| South Asian | 0.00342% | 29,235 |
| East Asian | 0.00226% | 44,164 |
| European (non-Finnish) | 0.00171% | 58,603 |
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
- IFNAR1
- Protein
- p.Val56=
- Coding
- c.168C>T
- MANE Select
- NM_000629
- dbSNP
- rs779146071
- Type
- single nucleotide variant
- Location
- chr21:33335615 (GRCh38)
- Gene constraint
- LOEUF 1.73 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.71 · 5 PDB
- Residue 56
- the fibronectin type-iii 1 domain
Similar variants
- IFNAR1 c.377-2A>G Likely pathogenic ★★ same type
- IFNAR1 p.Tyr250Ter Pathogenic/Likely pathogenic ★★ same type
- IFNAR1 p.Ala17Val Uncertain significance ★★ ⚠ same type
- IFNAR1 p.Ala408Val Uncertain significance ★★ ⚠ same type
- IFNAR1 p.Arg124His Uncertain significance ★★ ⚠ same type
- IFNAR1 p.Arg306His Uncertain significance ★★ ⚠ same type
- IFNAR1 p.Arg340Gly Uncertain significance ★★ ⚠ same type
- IFNAR1 p.Asn44His 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/ifnar1-p-val56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown