rs3596

Positions:

• chr12-95302644-A-G
• chr12-95302644-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017599.4(VEZT):​c.*1971A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,874 control chromosomes in the GnomAD database, including 18,154 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.48 (18154 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: VEZT NM_017599.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

VEZT (HGNC:18258): (vezatin, adherens junctions transmembrane protein) This gene encodes a transmembrane protein which has been localized to adherens junctions and shown to bind to myosin VIIA. Examination of expression of this gene in gastric cancer tissues have shown that expression is decreased which appears to be related to hypermethylation of the promoter. Expression of this gene may also be inhibited by binding of a specific microRNA to a target sequence in the 3' UTR of the transcripts. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

VEZT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VEZT	NM_017599.4	c.*1971A>G		3_prime_UTR_variant	12/12	ENST00000436874.6	NP_060069.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VEZT	ENST00000436874.6	c.*1971A>G		3_prime_UTR_variant	12/12	1	NM_017599.4	ENSP00000410083.1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73471 AN: 151756 Hom.: 18128 Cov.: 31

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.496

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.484 AC: 73547 AN: 151874 Hom.: 18154 Cov.: 31 AF XY: 0.475 AC XY: 35257 AN XY: 74214

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.497

Alfa AF: 0.481 Hom.: 16632

Bravo AF: 0.496

Asia WGS AF: 0.484 AC: 1678 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.072
DANN	Benign	0.58

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: rs3596; hg19: chr12-95696420;