VIM c.624+7A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
cataract 30
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.7, phastCons 0.95 |
| Non-coding constraint | Z 2.63 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 10.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,008 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,130 alleles · very rare
exomes 2/1,461,840 · genomes 0/152,290 · joint denominator
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.624+7A>C
- MANE Select
- NM_003380
- dbSNP
- rs376197279
- Type
- single nucleotide variant
- Location
- chr10:17230717 (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-624-plus-7a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown