Variant 5-77077343-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_032367.4(ZBED3):c.536C>G(p.Ala179Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00581 in 1,255,628 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 24 hom. )

Consequence

ZBED3
NM_032367.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.407

Variant links:

Genes affected

ZBED3 (HGNC:20711): (zinc finger BED-type containing 3) This gene belongs to a class of genes that arose through hAT DNA transposition and that encode regulatory proteins. This gene is upregulated in lung cancer tissues, where the encoded protein causes an accumulation of beta-catenin and enhanced lung cancer cell invasion. In addition, the encoded protein can be secreted and be involved in resistance to insulin. [provided by RefSeq, Jul 2016]

ZBED3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034475327).

BP6

Variant 5-77077343-G-C is Benign according to our data. Variant chr5-77077343-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2655548.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBED3	NM_032367.4 linkuse as main transcript	c.536C>G	p.Ala179Gly	missense_variant	3/3	ENST00000255198.3
ZBED3	NM_001329564.2 linkuse as main transcript	c.536C>G	p.Ala179Gly	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBED3	ENST00000255198.3 linkuse as main transcript	c.536C>G	p.Ala179Gly	missense_variant	3/3	1	NM_032367.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00416

AC:

627

AN:

150890

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00396

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00108

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00704

Gnomad OTH

AF:

0.00433

GnomAD3 exomes

AF:

0.00876

AC:

AN:

4678

Hom.:

AF XY:

0.00833

AC XY:

AN XY:

2882

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00592

Gnomad ASJ exome

AF:

0.00990

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00548

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0107

Gnomad OTH exome

AF:

0.00862

GnomAD4 exome

AF:

0.00604

AC:

6674

AN:

1104630

Hom.:

Cov.:

AF XY:

0.00600

AC XY:

3189

AN XY:

531364

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00416

Gnomad4 ASJ exome

AF:

0.00740

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00184

Gnomad4 FIN exome

AF:

0.00170

Gnomad4 NFE exome

AF:

0.00655

Gnomad4 OTH exome

AF:

0.00603

GnomAD4 genome

AF:

0.00415

AC:

627

AN:

150998

Hom.:

Cov.:

AF XY:

0.00358

AC XY:

264

AN XY:

73746

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00395

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00108

Gnomad4 NFE

AF:

0.00704

Gnomad4 OTH

AF:

0.00428

Alfa

AF:

0.00128

Hom.:

Bravo

AF:

0.00445

ExAC

AF:

0.000805

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

ZBED3: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.095

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.74

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.37

MetaRNN

Benign

0.0034

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-2.3

REVEL

Benign

0.037

Sift

Benign

0.39

Sift4G

Benign

0.36

Polyphen

0.85

Vest4

0.12

MVP

0.092

MPC

2.1

ClinPred

0.045

GERP RS

1.7

Varity_R

0.063

gMVP

0.013

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over