17-57979243-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGC

Variant names:

• chr17-57979243-TTGCTGC-T
• rs57786397
• NM_007146.3:c.1041_1046delGCAGCA

Variant summary

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

The NM_007146.3(VEZF1):​c.1041_1046delGCAGCA​(p.Gln348_Gln349del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000728 in 1,596,984 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q347Q) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0011 (0 hom., cov: 28)
  • Exomes 𝑓: 0.00069 (0 hom.)
• Consequence: VEZF1 NM_007146.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.34

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 160 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEZF1	NM_007146.3	c.1041_1046delGCAGCA	p.Gln348_Gln349del	disruptive_inframe_deletion	Exon 5 of 6	ENST00000581208.2	NP_009077.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VEZF1	ENST00000581208.2	c.1041_1046delGCAGCA	p.Gln348_Gln349del	disruptive_inframe_deletion	Exon 5 of 6	1	NM_007146.3	ENSP00000462337.1
VEZF1	ENST00000258963.7	c.495_500delGCAGCA	p.Gln166_Gln167del	disruptive_inframe_deletion	Exon 4 of 5	1		ENSP00000258963.3
VEZF1	ENST00000584396.5	c.1014_1019delGCAGCA	p.Gln339_Gln340del	disruptive_inframe_deletion	Exon 5 of 6	5		ENSP00000464687.1

Frequencies

GnomAD3 genomes AF: 0.00106 AC: 160 AN: 150644 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000727

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00147

Gnomad FIN AF: 0.0000959

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000710

Gnomad OTH AF: 0.00194

GnomAD4 exome AF: 0.000693 AC: 1002 AN: 1446228 Hom.: 0 AF XY: 0.000692 AC XY: 498 AN XY: 719474

Gnomad4 AFR exome AF: 0.00164

Gnomad4 AMR exome AF: 0.000609

Gnomad4 ASJ exome AF: 0.000775

Gnomad4 EAS exome AF: 0.0000509

Gnomad4 SAS exome AF: 0.000944

Gnomad4 FIN exome AF: 0.000342

Gnomad4 NFE exome AF: 0.000691

Gnomad4 OTH exome AF: 0.000637

GnomAD4 genome AF: 0.00106 AC: 160 AN: 150756 Hom.: 0 Cov.: 28 AF XY: 0.00105 AC XY: 77 AN XY: 73666

Gnomad4 AFR AF: 0.00218

Gnomad4 AMR AF: 0.000726

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00147

Gnomad4 FIN AF: 0.0000959

Gnomad4 NFE AF: 0.000710

Gnomad4 OTH AF: 0.00192

ClinVar

Not reported in ClinVar

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;