Variant 10-17229401-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003380.5(VIM):c.-22G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,587,024 control chromosomes in the GnomAD database, including 92,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 14765 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77351 hom. )

Consequence

VIM
NM_003380.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.09

Variant links:

Genes affected

VIM (HGNC:12692): (vimentin) This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]

VIM links:

VIM (HGNC:):

VIM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 10-17229401-G-C is Benign according to our data. Variant chr10-17229401-G-C is described in ClinVar as [Benign]. Clinvar id is 1277763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIM	NM_003380.5 linkuse as main transcript	c.-22G>C		5_prime_UTR_variant	2/10	ENST00000544301.7	NP_003371.2	P08670V9HWE1
VIM-AS1	NR_108061.1 linkuse as main transcript	n.585C>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIM	ENST00000544301 linkuse as main transcript	c.-22G>C		5_prime_UTR_variant	2/10	1	NM_003380.5	ENSP00000446007.1		P08670

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62814

AN:

151762

Hom.:

14721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.644

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.360

GnomAD3 exomes

AF:

0.344

AC:

70253

AN:

204226

Hom.:

13287

AF XY:

0.328

AC XY:

36988

AN XY:

112870

show subpopulations

Gnomad AFR exome

AF:

0.654

Gnomad AMR exome

AF:

0.479

Gnomad ASJ exome

AF:

0.191

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.367

Gnomad NFE exome

AF:

0.314

Gnomad OTH exome

AF:

0.315

GnomAD4 exome

AF:

0.321

AC:

460557

AN:

1435150

Hom.:

77351

Cov.:

AF XY:

0.316

AC XY:

225679

AN XY:

713324

show subpopulations

Gnomad4 AFR exome

AF:

0.656

Gnomad4 AMR exome

AF:

0.470

Gnomad4 ASJ exome

AF:

0.187

Gnomad4 EAS exome

AF:

0.262

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.363

Gnomad4 NFE exome

AF:

0.316

Gnomad4 OTH exome

AF:

0.322

GnomAD4 genome

AF:

0.414

AC:

62918

AN:

151874

Hom.:

14765

Cov.:

AF XY:

0.414

AC XY:

30696

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.644

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.373

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.361

Alfa

AF:

0.251

Hom.:

914

Bravo

AF:

0.432

Asia WGS

AF:

0.322

AC:

1119

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Cataract 30

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over