VIM c.-27C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.63%, amr) — too common for a highly-penetrant pathogenic allele
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 0.42 | GERP -3.4 |
| Overall | ||
| CADD | 11.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.63%
Admixed American · 3,263/57,924 alleles
Filtering AF
5.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.41%
Overall
0.22%
3,479/1,583,860 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 5.63% | 18 |
| Remaining individualsnot grpmax-eligible | 0.182% | 548 |
| African / African-American | 0.109% | 915 |
| European (non-Finnish) | 0.00188% | 53,238 |
| South Asian | 0.00113% | 88,198 |
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.-27C>T
- MANE Select
- NM_003380
- dbSNP
- rs200253669
- Type
- single nucleotide variant
- Location
- chr10:17229396 (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-minus-27c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown