Is VIM p.Asn128= (c.384T>C) pathogenic?

VIM p.Asn128= (c.384T>C) is classified Likely benign in VIM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-14). Ultra-rare (popmax 0.0522%, afr); Associated with cataract 30.

What condition is associated with VIM p.Asn128= (c.384T>C)?

VIM p.Asn128= (c.384T>C) is associated with cataract 30 (ClinVar).

How common is VIM p.Asn128= (c.384T>C) in the general population?

VIM p.Asn128= (c.384T>C) is ultra-rare (popmax 0.0522%, afr) (gnomAD).

VIM p.Asn128=

c.384T>C · rs147857896 · VCV1630176

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0522%, afr)

Conditions

cataract 30

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.9	GERP -1.1, phastCons 1
Overall
CADD	18.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0522% African / African-American · 39/74,752 alleles

Filtering AF 0.0392% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0346%

Overall 0.00263% 42/1,598,262 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0522%	1,917
Remaining individualsnot grpmax-eligible	0.00161%	61,986
European (non-Finnish)	0.000171%	586,304

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
Protein: p.Asn128=
Coding: c.384T>C
dbSNP: rs147857896
Type: single nucleotide variant
Location: chr10:17229806 (GRCh38)

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

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-p-asn128 (accessed [today's date]).

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