Variant chr19-36997153-T-G 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.1462T>G(p.Tyr488Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,586,450 control chromosomes in the GnomAD database, including 22,265 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 0.18 ( 2431 hom., cov: 32)

Exomes 𝑓: 0.16 ( 19834 hom. )

Consequence

ZNF568
ENST00000444991.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.62

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=0.0061773956).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
ZNF568	NM_001204838.2 linkuse as main transcript	c.1462T>G	p.Tyr488Asp	missense_variant	10/10
ZNF568	NM_001204839.2 linkuse as main transcript	c.1270T>G	p.Tyr424Asp	missense_variant	9/9
ZNF568	XM_017026772.2 linkuse as main transcript	c.1462T>G	p.Tyr488Asp	missense_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	UniProt
ZNF568	ENST00000444991.6 linkuse as main transcript	c.1462T>G	p.Tyr488Asp	missense_variant	10/10	1
ZNF568	ENST00000591887.1 linkuse as main transcript	n.1631T>G		non_coding_transcript_exon_variant	2/2	1
ZNF568	ENST00000455427.7 linkuse as main transcript	c.1270T>G	p.Tyr424Asp	missense_variant	9/9	2	Q3ZCX4-3

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26840

AN:

151810

Hom.:

2425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.172

AC:

36021

AN:

209504

Hom.:

3231

AF XY:

0.176

AC XY:

19947

AN XY:

113594

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.143

Gnomad ASJ exome

AF:

0.170

Gnomad EAS exome

AF:

0.172

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.164

AC:

234813

AN:

1434522

Hom.:

19834

Cov.:

AF XY:

0.166

AC XY:

118069

AN XY:

712058

show subpopulations

Gnomad4 AFR exome

AF:

0.209

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.185

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.168

GnomAD4 genome

AF:

0.177

AC:

26865

AN:

151928

Hom.:

2431

Cov.:

AF XY:

0.178

AC XY:

13232

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.169

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.152

Hom.:

2280

Bravo

AF:

0.175

TwinsUK

AF:

0.166

AC:

614

ALSPAC

AF:

0.168

AC:

647

ExAC

AF:

0.159

AC:

19087

Asia WGS

AF:

0.221

AC:

768

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.44

CADD

Uncertain

DANN

Uncertain

0.98

DEOGEN2

Benign

0.34

T;.;.;.

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.22

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.90

D;T;T;D

MetaRNN

Benign

0.0062

T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

PROVEAN

Pathogenic

-6.4

D;D;.;D

REVEL

Uncertain

0.30

Sift

Pathogenic

0.0

D;D;.;D

Sift4G

Pathogenic

0.0

D;D;D;D

Vest4

0.46, 0.47

ClinPred

0.048

GERP RS

3.9

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