VIM c.1229+89C>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.42%, afr) — 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 | ||
| Splice region | donor +89 | deep intronic (+89 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.053 | GERP -1.4 |
| Non-coding constraint | Z 1.84 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 3.508 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.42%
African / African-American · 4,573/71,206 alleles
Filtering AF
6.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.2%
Overall
0.389%
5,569/1,430,318 alleles · common
exomes 2,813/1,278,056 · genomes 2,756/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.42% | 16 |
| Ashkenazi Jewishnot grpmax-eligible | 0.61% | 164 |
| Middle Eastern | 0.602% | 166 |
| Remaining individualsnot grpmax-eligible | 0.534% | 187 |
| Admixed American | 0.394% | 254 |
| South Asian | 0.0324% | 3,084 |
| European (non-Finnish) | 0.024% | 4,162 |
| Finnishnot grpmax-eligible | 0.00169% | 59,204 |
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.1229+89C>G
- MANE Select
- NM_003380
- dbSNP
- rs74120324
- Type
- single nucleotide variant
- Location
- chr10:17235478 (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-1229-plus-89c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown