Variant rs1667354 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444991.6(ZNF568):c.479A>G(p.Asp160Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,534,716 control chromosomes in the GnomAD database, including 225,748 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 24509 hom., cov: 32)

Exomes 𝑓: 0.54 ( 201239 hom. )

Consequence

ZNF568
ENST00000444991.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.316

Variant links:

Genes affected

ZNF568 (HGNC:25392): (zinc finger protein 568) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic placenta morphogenesis and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF568 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.637041E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
ZNF568	NM_001204838.2 linkuse as main transcript	c.479A>G	p.Asp160Gly	missense_variant	8/10	NP_001191767.1
ZNF568	NM_001204839.2 linkuse as main transcript	c.287A>G	p.Asp96Gly	missense_variant	7/9	NP_001191768.1
ZNF568	XM_017026772.2 linkuse as main transcript	c.479A>G	p.Asp160Gly	missense_variant	8/10	XP_016882261.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
ZNF568	ENST00000444991.6 linkuse as main transcript	c.479A>G	p.Asp160Gly	missense_variant	8/10	1	ENSP00000389794
ZNF568	ENST00000591887.1 linkuse as main transcript	n.197A>G		non_coding_transcript_exon_variant	1/2	1
ZNF568	ENST00000455427.7 linkuse as main transcript	c.287A>G	p.Asp96Gly	missense_variant	7/9	2	ENSP00000413396	Q3ZCX4-3

Frequencies

GnomAD3 genomes

AF:

0.559

AC:

84876

AN:

151902

Hom.:

24471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.552

GnomAD3 exomes

AF:

0.510

AC:

70413

AN:

138030

Hom.:

18553

AF XY:

0.514

AC XY:

38348

AN XY:

74658

show subpopulations

Gnomad AFR exome

AF:

0.673

Gnomad AMR exome

AF:

0.487

Gnomad ASJ exome

AF:

0.457

Gnomad EAS exome

AF:

0.262

Gnomad SAS exome

AF:

0.567

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.530

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.537

AC:

741934

AN:

1382696

Hom.:

201239

Cov.:

AF XY:

0.537

AC XY:

366201

AN XY:

682232

show subpopulations

Gnomad4 AFR exome

AF:

0.676

Gnomad4 AMR exome

AF:

0.498

Gnomad4 ASJ exome

AF:

0.462

Gnomad4 EAS exome

AF:

0.289

Gnomad4 SAS exome

AF:

0.567

Gnomad4 FIN exome

AF:

0.530

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.532

GnomAD4 genome

AF:

0.559

AC:

84975

AN:

152020

Hom.:

24509

Cov.:

AF XY:

0.558

AC XY:

41464

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.536

Gnomad4 ASJ

AF:

0.461

Gnomad4 EAS

AF:

0.264

Gnomad4 SAS

AF:

0.571

Gnomad4 FIN

AF:

0.546

Gnomad4 NFE

AF:

0.527

Gnomad4 OTH

AF:

0.550

Alfa

AF:

0.517

Hom.:

32666

Bravo

AF:

0.560

TwinsUK

AF:

0.543

AC:

2012

ALSPAC

AF:

0.562

AC:

2166

ExAC

AF:

0.494

AC:

9608

Asia WGS

AF:

0.468

AC:

1629

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.014

T;.;.;.

Eigen

Benign

-0.61

Eigen_PC

Benign

-0.60

FATHMM_MKL

Benign

0.066

LIST_S2

Benign

0.18

T;T;T;T

MetaRNN

Benign

0.0000086

T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PROVEAN

Benign

-2.2

N;N;.;D

REVEL

Benign

0.051

Sift

Benign

0.20

T;T;.;D

Sift4G

Benign

0.15

T;T;T;D

Vest4

0.10, 0.048

ClinPred

0.0037

GERP RS

2.3

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over