IFITM5 p.Arg7=
c.21C>T · rs755699416 · VCV1202188
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, eas)
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 1.3 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 9.796 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
East Asian · 10/40,012 alleles
Filtering AF
0.0135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.00326%
49/1,500,884 alleles · ultra-rare
exomes 43/1,348,708 · genomes 6/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.025% | 4,001 |
| Finnishnot grpmax-eligible | 0.0087% | 11,498 |
| South Asian | 0.0079% | 12,657 |
| Admixed American | 0.00687% | 14,566 |
| African / African-American | 0.00565% | 17,689 |
| Remaining individualsnot grpmax-eligible | 0.00346% | 28,881 |
| European (non-Finnish) | 0.00169% | 59,184 |
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.Arg7=
- Coding
- c.21C>T
- MANE Select
- NM_001025295
- dbSNP
- rs755699416
- Type
- single nucleotide variant
- Location
- chr11:299470 (GRCh38)
- Gene constraint
- LOEUF 1.83 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.49
- Residue 7
- the 'disordered' region
Similar variants
- IFITM5 p.Arg7Cys Uncertain significance ★ ⚠ same residue
- IFITM5 p.Arg7His Likely 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-arg7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown