dbSNP rs2288421: 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:

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=-0.89).

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

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