Is VIM c.720+18C>T pathogenic?

VIM c.720+18C>T is classified Benign/Likely benign in VIM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-24). Low-frequency (popmax 4.67%, afr); Associated with cataract 30.

What condition is associated with VIM c.720+18C>T?

VIM c.720+18C>T is associated with cataract 30 (ClinVar).

How common is VIM c.720+18C>T in the general population?

VIM c.720+18C>T is low-frequency (popmax 4.67%, afr) (gnomAD).

VIM c.720+18C>T

rs7096093 · VCV1316436

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.67%, afr)

Conditions

cataract 30

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +18	near-intronic (+18 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.6	GERP -3.7
Non-coding constraint	Z 1.81	1 kb window · o/e 0.88 · regional · uncalibrated
Overall
CADD	0.26	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.67% African / African-American · 3,507/75,022 alleles

Filtering AF 4.55% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.49%

Overall 0.258% 4,168/1,614,058 alleles · low-frequency exomes 2,154/1,461,836 · genomes 2,014/152,222 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.67%	21
Remaining individualsnot grpmax-eligible	0.354%	283
Admixed American	0.353%	283
East Asian	0.192%	522
Middle Eastern	0.181%	551
South Asian	0.0209%	4,793
European (non-Finnish)	0.00949%	10,536

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.720+18C>T
MANE Select: NM_003380
dbSNP: rs7096093
Type: single nucleotide variant
Location: chr10:17233700 (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-720-plus-18c-t (accessed [today's date]).

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