Genetic Variant ZNF160:c.*24A>G (chr19-53068053-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001322131.2(ZNF160):c.*24A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,565,046 control chromosomes in the GnomAD database, including 62,914 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 0.23 ( 5007 hom., cov: 32)

Exomes 𝑓: 0.28 ( 57907 hom. )

Consequence

ZNF160
NM_001322131.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

17 publications found

Variant links:

Genes affected

ZNF160 (HGNC:12948): (zinc finger protein 160) The protein encoded by this gene is a Kruppel-related zinc finger protein which is characterized by the presence of an N-terminal repressor domain, the Kruppel-associated box (KRAB). The KRAB domain is a potent repressor of transcription; thus this protein may function in transcription regulation. Multiple transcript variants have been found for this gene. [provided by RefSeq, Apr 2016]

ZNF160 links:

ENSG00000306331 (HGNC:):

ENSG00000306331 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF160	NM_001322131.2 link	c.*24A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000683776.1	NP_001309060.1	Q9HCG1-1A0A024R4Q2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF160	ENST00000683776.1 link	c.*24A>G		3_prime_UTR_variant	Exon 6 of 6		NM_001322131.2	ENSP00000507845.1		Q9HCG1-1

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35159

AN:

151994

Hom.:

4999

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0772

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.235

GnomAD2 exomes

AF:

0.268

AC:

57486

AN:

214510

AF XY:

0.265

show subpopulations

Gnomad AFR exome

AF:

0.0671

Gnomad AMR exome

AF:

0.358

Gnomad ASJ exome

AF:

0.266

Gnomad EAS exome

AF:

0.300

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.292

Gnomad OTH exome

AF:

0.281

GnomAD4 exome

AF:

0.281

AC:

397208

AN:

1412934

Hom.:

57907

Cov.:

AF XY:

0.276

AC XY:

192709

AN XY:

697362

show subpopulations

African (AFR)

AF:

0.0653

AC:

2115

AN:

32368

American (AMR)

AF:

0.353

AC:

13974

AN:

39602

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

6050

AN:

22616

East Asian (EAS)

AF:

0.328

AC:

12902

AN:

39286

South Asian (SAS)

AF:

0.128

AC:

9909

AN:

77224

European-Finnish (FIN)

AF:

0.295

AC:

15256

AN:

51638

Middle Eastern (MID)

AF:

0.248

AC:

1141

AN:

4598

European-Non Finnish (NFE)

AF:

0.294

AC:

320180

AN:

1087390

Other (OTH)

AF:

0.269

AC:

15681

AN:

58212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

13749

27497

41246

54994

68743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10750

21500

32250

43000

53750

<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:

0.231

AC:

35176

AN:

152112

Hom.:

5007

Cov.:

AF XY:

0.234

AC XY:

17394

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0770

AC:

3197

AN:

41528

American (AMR)

AF:

0.354

AC:

5406

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

944

AN:

3472

East Asian (EAS)

AF:

0.292

AC:

1510

AN:

5174

South Asian (SAS)

AF:

0.133

AC:

642

AN:

4826

European-Finnish (FIN)

AF:

0.307

AC:

3243

AN:

10560

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19327

AN:

67972

Other (OTH)

AF:

0.234

AC:

495

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1322

2643

3965

5286

6608

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.271

Hom.:

10492

Bravo

AF:

0.231

Asia WGS

AF:

0.194

AC:

676

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.60

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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