Genetic Variant VEZF1:p.Gln349dup (chr17-57979243-T-TTGC) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3BA1

The NM_007146.3(VEZF1):c.1044_1046dupGCA(p.Gln349dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,591,096 control chromosomes in the GnomAD database, including 6,049 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 917 hom., cov: 28)

Exomes 𝑓: 0.11 ( 5132 hom. )

Consequence

VEZF1
NM_007146.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_007146.3

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEZF1	NM_007146.3 link	c.1044_1046dupGCA	p.Gln349dup	disruptive_inframe_insertion	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.1044_1046dupGCA	p.Gln349dup	disruptive_inframe_insertion	Exon 5 of 6	1	NM_007146.3	ENSP00000462337.1	Q14119
VEZF1	ENST00000258963.7 link	c.498_500dupGCA	p.Gln167dup	disruptive_inframe_insertion	Exon 4 of 5	1		ENSP00000258963.3	J9JIC7
VEZF1	ENST00000584396.5 link	c.1017_1019dupGCA	p.Gln340dup	disruptive_inframe_insertion	Exon 5 of 6	5		ENSP00000464687.1	J3QSH4

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16587

AN:

150584

Hom.:

916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.0777

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.0294

Gnomad SAS

AF:

0.0770

Gnomad FIN

AF:

0.0732

Gnomad MID

AF:

0.105

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.108

AC:

155640

AN:

1440400

Hom.:

5132

Cov.:

AF XY:

0.108

AC XY:

77060

AN XY:

716616

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0567

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.0232

Gnomad4 SAS exome

AF:

0.0833

Gnomad4 FIN exome

AF:

0.0771

Gnomad4 NFE exome

AF:

0.116

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.110

AC:

16588

AN:

150696

Hom.:

917

Cov.:

AF XY:

0.105

AC XY:

7723

AN XY:

73638

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.0776

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.0293

Gnomad4 SAS

AF:

0.0771

Gnomad4 FIN

AF:

0.0732

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.105

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over