IFITM5 p.Pro96=
c.288G>A · rs149676171 · VCV1533820
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, sas)
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 -20 | GERP -2.6 |
| Overall | ||
| CADD | 0.281 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
South Asian · 45/91,088 alleles
Filtering AF
0.0379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00651%
105/1,613,374 alleles · ultra-rare
exomes 92/1,461,038 · genomes 13/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0494% | 2,024 |
| African / African-American | 0.0147% | 6,824 |
| East Asian | 0.00668% | 14,961 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.00356% | 28,095 |
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
- IFITM5
- Protein
- p.Pro96=
- Coding
- c.288G>A
- MANE Select
- NM_001025295
- dbSNP
- rs149676171
- Type
- single nucleotide variant
- Location
- chr11:298612 (GRCh38)
- Gene constraint
- LOEUF 1.83 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.49
Similar variants
- IFITM5 p.Pro96Leu Uncertain significance ★★ ⚠ same residue
- IFITM5 p.Pro96_Leu99del Benign ★ same residue
- IFITM5 c.-14C>T Pathogenic ★★ same type
- IFITM5 p.Ser40Leu Pathogenic ★★ same type
- IFITM5 p.Ser40Trp Pathogenic/Likely pathogenic ★★ same type
- IFITM5 p.Ala112Gly Uncertain significance ★★ ⚠ same type
- IFITM5 p.Ala12Val Uncertain significance ★★ ⚠ same type
- IFITM5 p.Ala23Val 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/ifitm5-p-pro96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown