Genetic Variant ZNF160:c.*463G>A (chr19-53067614-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001322131.2(ZNF160):c.*463G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 154,218 control chromosomes in the GnomAD database, including 15,393 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 0.43 ( 15250 hom., cov: 32)

Exomes 𝑓: 0.33 ( 143 hom. )

Consequence

ZNF160
NM_001322131.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

10 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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new If you want to explore the variant's impact on the transcript NM_001322131.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322131.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF160	NM_001322131.2	MANE Select	c.*463G>A	3_prime_UTR	Exon 6 of 6	NP_001309060.1	Q9HCG1-1
ZNF160	NM_001102603.2		c.*463G>A	3_prime_UTR	Exon 7 of 7	NP_001096073.1	Q9HCG1-1
ZNF160	NM_001322128.2		c.*463G>A	3_prime_UTR	Exon 7 of 7	NP_001309057.1	Q9HCG1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF160	ENST00000683776.1	MANE Select	c.*463G>A	3_prime_UTR	Exon 6 of 6	ENSP00000507845.1	Q9HCG1-1
ZNF160	ENST00000418871.5	TSL:1	c.*463G>A	3_prime_UTR	Exon 6 of 6	ENSP00000409597.1	Q9HCG1-1
ZNF160	ENST00000599056.5	TSL:1	c.*463G>A	3_prime_UTR	Exon 7 of 7	ENSP00000470961.1	Q9HCG1-1

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64877

AN:

151880

Hom.:

15205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.624

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.417

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.332

AC:

737

AN:

2220

Hom.:

143

Cov.:

AF XY:

0.319

AC XY:

338

AN XY:

1060

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AF:

0.365

AC:

105

AN:

288

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

AN:

East Asian (EAS)

AF:

0.0714

AC:

AN:

South Asian (SAS)

AF:

0.337

AC:

AN:

European-Finnish (FIN)

AF:

0.260

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.322

AC:

512

AN:

1588

Other (OTH)

AF:

0.366

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

108

135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.427

AC:

64977

AN:

151998

Hom.:

15250

Cov.:

AF XY:

0.420

AC XY:

31232

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.625

AC:

25902

AN:

41456

American (AMR)

AF:

0.399

AC:

6086

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.417

AC:

1446

AN:

3468

East Asian (EAS)

AF:

0.109

AC:

560

AN:

5158

South Asian (SAS)

AF:

0.321

AC:

1545

AN:

4814

European-Finnish (FIN)

AF:

0.321

AC:

3392

AN:

10558

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24794

AN:

67974

Other (OTH)

AF:

0.426

AC:

899

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1797

3595

5392

7190

8987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

582

1164

1746

2328

2910

<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:

0.385

Hom.:

35832

Bravo

AF:

0.440

Asia WGS

AF:

0.281

AC:

975

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.9

(source)

DANN

Benign

0.51

PhyloP100

-1.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over