17-57979243-TTGCTGCTGCTGC-T

Position:

• chr17-57979243-TTGCTGCTGCTGC-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_007146.3(VEZF1):​c.1035_1046del​(p.Gln351_Gln354del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000818 in 1,597,060 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.00081 (0 hom., cov: 28)
  • Exomes 𝑓: 0.00082 (2 hom.)
• Consequence: VEZF1 NM_007146.3 inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 5.35

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_007146.3
• BS2: High AC in GnomAd4 at 122 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VEZF1	NM_007146.3	c.1035_1046del	p.Gln351_Gln354del	inframe_deletion	5/6	ENST00000581208.2	NP_009077.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VEZF1	ENST00000581208.2	c.1035_1046del	p.Gln351_Gln354del	inframe_deletion	5/6	1	NM_007146.3	ENSP00000462337	P2
VEZF1	ENST00000258963.7	c.491_502del	p.Gln170_Gln173del	inframe_deletion	4/5	1		ENSP00000258963
VEZF1	ENST00000584396.5	c.1008_1019del	p.Gln342_Gln345del	inframe_deletion	5/6	5		ENSP00000464687	A2

Frequencies

GnomAD3 genomes AF: 0.000810 AC: 122 AN: 150648 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000198

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.000421

Gnomad FIN AF: 0.0000959

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000665

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000819 AC: 1185 AN: 1446300 Hom.: 2 AF XY: 0.000848 AC XY: 610 AN XY: 719506

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.000474

Gnomad4 ASJ exome AF: 0.0000387

Gnomad4 EAS exome AF: 0.000636

Gnomad4 SAS exome AF: 0.00243

Gnomad4 FIN exome AF: 0.0000570

Gnomad4 NFE exome AF: 0.000740

Gnomad4 OTH exome AF: 0.000989

GnomAD4 genome AF: 0.000809 AC: 122 AN: 150760 Hom.: 0 Cov.: 28 AF XY: 0.000787 AC XY: 58 AN XY: 73668

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.000198

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.000421

Gnomad4 FIN AF: 0.0000959

Gnomad4 NFE AF: 0.000665

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000831

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57786397; hg19: chr17-56056604;