Variant rs1667363 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.1273A>T(p.Ser425Cys) variant causes a missense change. The variant allele was found at a frequency of 0.527 in 1,539,246 control chromosomes in the GnomAD database, including 215,871 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/13 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 0.53 ( 22004 hom., cov: 31)

Exomes 𝑓: 0.53 ( 193867 hom. )

Consequence

ZNF568
ENST00000444991.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.67

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=1.8989978E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
ZNF568	NM_001204838.2 linkuse as main transcript	c.1273A>T	p.Ser425Cys	missense_variant	10/10
ZNF568	NM_001204839.2 linkuse as main transcript	c.1081A>T	p.Ser361Cys	missense_variant	9/9
ZNF568	XM_017026772.2 linkuse as main transcript	c.1273A>T	p.Ser425Cys	missense_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	UniProt
ZNF568	ENST00000444991.6 linkuse as main transcript	c.1273A>T	p.Ser425Cys	missense_variant	10/10	1
ZNF568	ENST00000591887.1 linkuse as main transcript	n.1442A>T		non_coding_transcript_exon_variant	2/2	1
ZNF568	ENST00000455427.7 linkuse as main transcript	c.1081A>T	p.Ser361Cys	missense_variant	9/9	2	Q3ZCX4-3

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

80650

AN:

151264

Hom.:

21969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.524

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.538

GnomAD3 exomes

AF:

0.509

AC:

76550

AN:

150466

Hom.:

20009

AF XY:

0.513

AC XY:

41375

AN XY:

80730

show subpopulations

Gnomad AFR exome

AF:

0.629

Gnomad AMR exome

AF:

0.485

Gnomad ASJ exome

AF:

0.446

Gnomad EAS exome

AF:

0.268

Gnomad SAS exome

AF:

0.560

Gnomad FIN exome

AF:

0.520

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.514

GnomAD4 exome

AF:

0.526

AC:

729690

AN:

1387862

Hom.:

193867

Cov.:

AF XY:

0.526

AC XY:

360669

AN XY:

685438

show subpopulations

Gnomad4 AFR exome

AF:

0.614

Gnomad4 AMR exome

AF:

0.493

Gnomad4 ASJ exome

AF:

0.449

Gnomad4 EAS exome

AF:

0.291

Gnomad4 SAS exome

AF:

0.557

Gnomad4 FIN exome

AF:

0.511

Gnomad4 NFE exome

AF:

0.532

Gnomad4 OTH exome

AF:

0.520

GnomAD4 genome

AF:

0.533

AC:

80747

AN:

151384

Hom.:

22004

Cov.:

AF XY:

0.533

AC XY:

39395

AN XY:

73976

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.524

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.264

Gnomad4 SAS

AF:

0.558

Gnomad4 FIN

AF:

0.512

Gnomad4 NFE

AF:

0.517

Gnomad4 OTH

AF:

0.537

Alfa

AF:

0.511

Hom.:

3697

Bravo

AF:

0.536

TwinsUK

AF:

0.533

AC:

1976

ALSPAC

AF:

0.554

AC:

2134

ExAC

AF:

0.464

AC:

46611

Asia WGS

AF:

0.456

AC:

1585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.055

DEOGEN2

Benign

0.049

T;.;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.0092

LIST_S2

Benign

0.066

T;T;T;T

MetaRNN

Benign

0.000019

T;T;T;T

MetaSVM

Benign

-0.96

MutationTaster

Benign

0.97

PROVEAN

Benign

9.3

N;N;.;N

REVEL

Benign

0.12

Sift

Benign

1.0

T;T;.;T

Sift4G

Benign

1.0

T;T;T;T

Vest4

0.14, 0.12

ClinPred

0.0033

GERP RS

3.7

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