VIM c.*55C>T
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.95%, mid)
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 -0.21 | GERP -4 |
| Non-coding constraint | Z -0.97 | 1 kb window · o/e 1.07 · regional · uncalibrated |
| Overall | ||
| CADD | 2.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.95%
Middle Eastern · 214/5,416 alleles
Filtering AF
3.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.35%
Overall
1.62%
25,119/1,552,870 alleles · low-frequency
exomes 22,923/1,400,796 · genomes 2,196/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.95% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 2.88% | 35 |
| European (non-Finnish) | 1.8% | 56 |
| Remaining individualsnot grpmax-eligible | 1.69% | 59 |
| Admixed American | 1.56% | 64 |
| Finnishnot grpmax-eligible | 1.37% | 73 |
| South Asian | 0.604% | 165 |
| African / African-American | 0.511% | 196 |
| East Asian | 0.00452% | 22,144 |
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
- VIM
- Coding
- c.*55C>T
- MANE Select
- NM_003380
- dbSNP
- rs12667
- Type
- single nucleotide variant
- Location
- chr10:17237326 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 78.05 · 26 PDB
Similar variants
- VIM p.Arg45His Uncertain significance ★★ ⚠ same type
- VIM p.Asp360Glu Uncertain significance ★★ ⚠ same type
- VIM p.Leu164Val Uncertain significance ★★ ⚠ same type
- VIM p.Thr458Ala Uncertain significance ★★ ⚠ same type
- VIM p.Val272Ile Uncertain significance ★★ ⚠ same type
- VIM c.1008+18A>G Benign/Likely benign ★★ same type
- VIM c.1008+99G>A Benign ★★ same type
- VIM c.1009-10C>T Benign ★★ 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/vim-c-star-55c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown