VIM c.-22G>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 64.9%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
cataract 30
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 -0.91 | GERP -3.3 |
| Overall | ||
| CADD | 10.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
64.9%
African / African-American · 48,123/74,102 alleles
Filtering AF
64.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 64.3%
Overall
33%
523,475/1,587,024 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 64.9% | 2 |
| Admixed American | 45.8% | 2 |
| Amishnot grpmax-eligible | 44.4% | 2 |
| Finnishnot grpmax-eligible | 36.5% | 3 |
| Remaining individualsnot grpmax-eligible | 32.3% | 3 |
| European (non-Finnish) | 31.6% | 3 |
| East Asian | 26.4% | 4 |
| South Asian | 23.4% | 4 |
| Middle Eastern | 18.9% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 18.9% | 5 |
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.-22G>C
- MANE Select
- NM_003380
- dbSNP
- rs3758410
- Type
- single nucleotide variant
- Location
- chr10:17229401 (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 condition
- VIM p.Asp360Glu Uncertain significance ★★ ⚠ same condition
- VIM p.Leu164Val Uncertain significance ★★ ⚠ same condition
- VIM p.Thr458Ala Uncertain significance ★★ ⚠ same condition
- VIM p.Val272Ile Uncertain significance ★★ ⚠ same condition
- VIM c.1008+18A>G Benign/Likely benign ★★ same condition
- VIM c.1009-10C>T Benign ★★ same condition
- VIM c.1360-18G>T Likely benign ★★ same condition
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-22g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown