Genetic Variant ZNF568:n.2141C>G (chr19-36997663-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000591887.1(ZNF568):n.2141C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,225,206 control chromosomes in the GnomAD database, including 69,370 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 0.33 ( 8603 hom., cov: 31)

Exomes 𝑓: 0.34 ( 60767 hom. )

Consequence

ZNF568
ENST00000591887.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

6 publications found

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:

ENSG00000291239 (HGNC:):

ENSG00000291239 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ZNF568	NM_001204838.2 link	c.*64C>G	3_prime_UTR_variant	Exon 10 of 10	NP_001191767.1	Q3ZCX4C9JLX5Q96AZ9
ZNF568	NM_001204839.2 link	c.*64C>G	3_prime_UTR_variant	Exon 9 of 9	NP_001191768.1	Q3ZCX4-3Q96AZ9
ZNF568	XM_017026772.2 link	c.*64C>G	3_prime_UTR_variant	Exon 10 of 10	XP_016882261.1	C9JLX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291239	ENST00000706165.1 link	c.*64C>G		3_prime_UTR_variant	Exon 12 of 12			ENSP00000516244.1		C9JLX5

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50375

AN:

151680

Hom.:

8587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.0952

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.322

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.328

GnomAD2 exomes

AF:

0.325

AC:

45801

AN:

141016

AF XY:

0.325

show subpopulations

Gnomad AFR exome

AF:

0.320

Gnomad AMR exome

AF:

0.333

Gnomad ASJ exome

AF:

0.274

Gnomad EAS exome

AF:

0.0917

Gnomad FIN exome

AF:

0.354

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.343

GnomAD4 exome

AF:

0.336

AC:

360226

AN:

1073408

Hom.:

60767

Cov.:

AF XY:

0.336

AC XY:

182320

AN XY:

542482

show subpopulations

African (AFR)

AF:

0.304

AC:

7524

AN:

24778

American (AMR)

AF:

0.337

AC:

11897

AN:

35266

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

6259

AN:

23264

East Asian (EAS)

AF:

0.105

AC:

3625

AN:

34562

South Asian (SAS)

AF:

0.314

AC:

22773

AN:

72434

European-Finnish (FIN)

AF:

0.343

AC:

12187

AN:

35540

Middle Eastern (MID)

AF:

0.317

AC:

1617

AN:

5106

European-Non Finnish (NFE)

AF:

0.351

AC:

278693

AN:

794808

Other (OTH)

AF:

0.328

AC:

15651

AN:

47650

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

10005

20010

30014

40019

50024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7728

15456

23184

30912

38640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.332

AC:

50442

AN:

151798

Hom.:

8603

Cov.:

AF XY:

0.331

AC XY:

24550

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.321

AC:

13257

AN:

41330

American (AMR)

AF:

0.344

AC:

5254

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3470

East Asian (EAS)

AF:

0.0955

AC:

492

AN:

5154

South Asian (SAS)

AF:

0.297

AC:

1424

AN:

4802

European-Finnish (FIN)

AF:

0.342

AC:

3603

AN:

10538

Middle Eastern (MID)

AF:

0.325

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.362

AC:

24594

AN:

67928

Other (OTH)

AF:

0.328

AC:

692

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1716

3432

5148

6864

8580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

510

1020

1530

2040

2550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.224

Hom.:

724

Bravo

AF:

0.332

Asia WGS

AF:

0.232

AC:

807

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.7

(source)

DANN

Benign

0.71

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over