chr17-57979243-TTGC-T

Variant names:

• chr17-57979243-TTGC-T
• rs57786397
• NM_007146.3:c.1044_1046delGCA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3 BA1

The NM_007146.3(VEZF1):​c.1044_1046delGCA​(p.Gln349del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,584,348 control chromosomes in the GnomAD database, including 272 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.029 (143 hom., cov: 28)
  • Exomes 𝑓: 0.0099 (129 hom.)
• Consequence: VEZF1 NM_007146.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478

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 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 = 0.0797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEZF1	NM_007146.3	c.1044_1046delGCA	p.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.1044_1046delGCA	p.Gln349del	disruptive_inframe_deletion	Exon 5 of 6	1	NM_007146.3	ENSP00000462337.1
VEZF1	ENST00000258963.7	c.498_500delGCA	p.Gln167del	disruptive_inframe_deletion	Exon 4 of 5	1		ENSP00000258963.3
VEZF1	ENST00000584396.5	c.1017_1019delGCA	p.Gln340del	disruptive_inframe_deletion	Exon 5 of 6	5		ENSP00000464687.1

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4341 AN: 150604 Hom.: 143 Cov.: 28

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0104

Gnomad ASJ AF: 0.00377

Gnomad EAS AF: 0.00947

Gnomad SAS AF: 0.00463

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00893

Gnomad OTH AF: 0.0155

GnomAD4 exome AF: 0.00993 AC: 14231 AN: 1433632 Hom.: 129 AF XY: 0.00956 AC XY: 6817 AN XY: 713114

Gnomad4 AFR exome AF: 0.0824

Gnomad4 AMR exome AF: 0.00834

Gnomad4 ASJ exome AF: 0.00243

Gnomad4 EAS exome AF: 0.00647

Gnomad4 SAS exome AF: 0.00524

Gnomad4 FIN exome AF: 0.00966

Gnomad4 NFE exome AF: 0.00838

Gnomad4 OTH exome AF: 0.0123

GnomAD4 genome AF: 0.0288 AC: 4344 AN: 150716 Hom.: 143 Cov.: 28 AF XY: 0.0279 AC XY: 2052 AN XY: 73646

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.0104

Gnomad4 ASJ AF: 0.00377

Gnomad4 EAS AF: 0.00950

Gnomad4 SAS AF: 0.00463

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.00895

Gnomad4 OTH AF: 0.0153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs57786397; hg19: chr17-56056604;