VIM c.624+210del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 28%, sas) — 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 +210 | deep intronic (+210 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -0.79 |
| Non-coding constraint | Z 2.63 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 4.676 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
28%
South Asian · 11,284/40,320 alleles
Filtering AF
27.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 27.4%
Overall
22.7%
100,170/441,294 alleles · common
exomes 91,254/301,010 · genomes 8,916/140,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 28% | 4 |
| Remaining individualsnot grpmax-eligible | 27.2% | 4 |
| European (non-Finnish) | 25.1% | 4 |
| Middle Eastern | 24.9% | 4 |
| Finnishnot grpmax-eligible | 23.2% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 23.1% | 4 |
| East Asian | 22.6% | 4 |
| Admixed American | 17.3% | 6 |
| Amishnot grpmax-eligible | 10.8% | 9 |
| African / African-American | 6.72% | 15 |
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+210del
- MANE Select
- NM_003380
- dbSNP
- rs397844940
- Type
- Deletion
- Location
- chr10:17230905 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 78.05 · 26 PDB
Similar variants
- VIM c.1360-7del Benign/Likely 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-624-plus-210del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown