Is VIM c.882+20G>A pathogenic?

VIM c.882+20G>A is classified Likely benign in VIM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-22). Ultra-rare (popmax 0.0208%, nfe); Associated with cataract 30.

What condition is associated with VIM c.882+20G>A?

VIM c.882+20G>A is associated with cataract 30 (ClinVar).

How common is VIM c.882+20G>A in the general population?

VIM c.882+20G>A is ultra-rare (popmax 0.0208%, nfe) (gnomAD).

VIM c.882+20G>A

rs370279416 · VCV2849423

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0208%, nfe)

Conditions

cataract 30

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +20	near-intronic (+20 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.15	GERP -3.3
Non-coding constraint	Z 1.81	1 kb window · o/e 0.88 · regional · uncalibrated
Overall
CADD	0.874	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0208% European (non-Finnish) · 245/1,175,312 alleles

Filtering AF 0.0187% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0178%

Overall 0.0165% 264/1,604,494 alleles · ultra-rare exomes 258/1,452,260 · genomes 6/152,234 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0208%	4,797
Remaining individualsnot grpmax-eligible	0.0129%	7,777
South Asian	0.00781%	12,809
Admixed American	0.00345%	29,024
Finnishnot grpmax-eligible	0.00157%	63,532
African / African-American	0.00134%	74,830

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.882+20G>A
MANE Select: NM_003380
dbSNP: rs370279416
Type: single nucleotide variant
Location: chr10:17233951 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 78.05 · 26 PDB

Full VIM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cataract 30 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-882-plus-20g-a (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown