VIM c.1008+99G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.5%, 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 +99 | deep intronic (+99 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3.5 |
| Non-coding constraint | Z 1.46 | 1 kb window · o/e 0.90 · regional · uncalibrated |
| Overall | ||
| CADD | 0.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.5%
African / African-American · 7,703/73,370 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.2%
Overall
0.553%
8,491/1,535,058 alleles · common
exomes 4,027/1,382,786 · genomes 4,464/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.5% | 10 |
| Remaining individualsnot grpmax-eligible | 0.591% | 169 |
| Admixed American | 0.575% | 174 |
| Middle Eastern | 0.313% | 320 |
| South Asian | 0.0115% | 8,707 |
| European (non-Finnish) | 0.00804% | 12,434 |
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.1008+99G>A
- MANE Select
- NM_003380
- dbSNP
- rs75620192
- Type
- single nucleotide variant
- Location
- chr10:17234917 (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.1009-10C>T Benign ★★ same type
- VIM c.1229+115G>A 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-1008-plus-99g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown