Genetic Variant VEZF1:p.Gln345_Gln349del (chr17-57979243-TTGCTGCTGCTGCTGC-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2

The NM_007146.3(VEZF1):c.1032_1046delGCAGCAGCAGCAGCA(p.Gln345_Gln349del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00308 in 1,597,004 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 0 hom., cov: 28)

Exomes 𝑓: 0.0032 ( 8 hom. )

Consequence

VEZF1
NM_007146.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 5.35

Variant links:

Genes affected

VEZF1 (HGNC:12949): (vascular endothelial zinc finger 1) Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. ZNF161 is a C2H2-type zinc finger protein (Koyano-Nakagawa et al., 1994 [PubMed 8035792]). See MIM 603971 for general information on zinc finger proteins.[supplied by OMIM, Sep 2008]

VEZF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_007146.3

BP6

Variant 17-57979243-TTGCTGCTGCTGCTGC-T is Benign according to our data. Variant chr17-57979243-TTGCTGCTGCTGCTGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647952.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 330 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEZF1	NM_007146.3 link	c.1032_1046delGCAGCAGCAGCAGCA	p.Gln345_Gln349del	disruptive_inframe_deletion	Exon 5 of 6	ENST00000581208.2	NP_009077.2	Q14119

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
VEZF1	ENST00000581208.2 link	c.1032_1046delGCAGCAGCAGCAGCA	p.Gln345_Gln349del	disruptive_inframe_deletion	Exon 5 of 6	1	NM_007146.3	ENSP00000462337.1	Q14119
VEZF1	ENST00000258963.7 link	c.486_500delGCAGCAGCAGCAGCA	p.Gln163_Gln167del	disruptive_inframe_deletion	Exon 4 of 5	1		ENSP00000258963.3	J9JIC7
VEZF1	ENST00000584396.5 link	c.1005_1019delGCAGCAGCAGCAGCA	p.Gln336_Gln340del	disruptive_inframe_deletion	Exon 5 of 6	5		ENSP00000464687.1	J3QSH4

Frequencies

GnomAD3 genomes

AF:

0.00218

AC:

329

AN:

150642

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000981

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.000794

Gnomad ASJ

AF:

0.00406

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.00421

Gnomad FIN

AF:

0.00173

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00319

Gnomad OTH

AF:

0.00145

GnomAD4 exome

AF:

0.00317

AC:

4588

AN:

1446250

Hom.:

AF XY:

0.00314

AC XY:

2257

AN XY:

719484

show subpopulations

Gnomad4 AFR exome

AF:

0.000942

Gnomad4 AMR exome

AF:

0.00131

Gnomad4 ASJ exome

AF:

0.00325

Gnomad4 EAS exome

AF:

0.000407

Gnomad4 SAS exome

AF:

0.00316

Gnomad4 FIN exome

AF:

0.00110

Gnomad4 NFE exome

AF:

0.00356

Gnomad4 OTH exome

AF:

0.00235

GnomAD4 genome

AF:

0.00219

AC:

330

AN:

150754

Hom.:

Cov.:

AF XY:

0.00200

AC XY:

147

AN XY:

73664

show subpopulations

Gnomad4 AFR

AF:

0.000978

Gnomad4 AMR

AF:

0.000792

Gnomad4 ASJ

AF:

0.00406

Gnomad4 EAS

AF:

0.000775

Gnomad4 SAS

AF:

0.00421

Gnomad4 FIN

AF:

0.00173

Gnomad4 NFE

AF:

0.00319

Gnomad4 OTH

AF:

0.00144

Bravo

AF:

0.00202

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

VEZF1-related disorder

Benign:1

Apr 06, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Jun 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

VEZF1: BP3 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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