Variant 2-218638390-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001379659.1(ZNF142):c.5613G>A(p.Glu1871=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,533,196 control chromosomes in the GnomAD database, including 1,583 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 344 hom., cov: 32)

Exomes 𝑓: 0.038 ( 1239 hom. )

Consequence

ZNF142
NM_001379659.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.467

Variant links:

Genes affected

ZNF142 (HGNC:12927): (zinc finger protein 142) The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

ZNF142 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 2-218638390-C-T is Benign according to our data. Variant chr2-218638390-C-T is described in ClinVar as [Benign]. Clinvar id is 1254978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.467 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF142	NM_001379659.1 linkuse as main transcript	c.5613G>A	p.Glu1871=	synonymous_variant	11/11	ENST00000411696.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
ZNF142	ENST00000411696.7 linkuse as main transcript	c.5613G>A	p.Glu1871=	synonymous_variant	11/11	5	NM_001379659.1	P1
ZNF142	ENST00000449707.5 linkuse as main transcript	c.5013G>A	p.Glu1671=	synonymous_variant	10/10	1
ZNF142	ENST00000450765.5 linkuse as main transcript	c.*4838G>A		3_prime_UTR_variant, NMD_transcript_variant	11/11	1
ZNF142	ENST00000433921.5 linkuse as main transcript	c.*4838G>A		3_prime_UTR_variant, NMD_transcript_variant	11/11	2

Frequencies

GnomAD3 genomes

AF:

0.0564

AC:

8580

AN:

152146

Hom.:

343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0313

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.0441

Gnomad FIN

AF:

0.0271

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0339

Gnomad OTH

AF:

0.0516

GnomAD3 exomes

AF:

0.0454

AC:

8621

AN:

189866

Hom.:

272

AF XY:

0.0440

AC XY:

4423

AN XY:

100558

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.0209

Gnomad ASJ exome

AF:

0.0348

Gnomad EAS exome

AF:

0.114

Gnomad SAS exome

AF:

0.0427

Gnomad FIN exome

AF:

0.0308

Gnomad NFE exome

AF:

0.0340

Gnomad OTH exome

AF:

0.0370

GnomAD4 exome

AF:

0.0377

AC:

52103

AN:

1380932

Hom.:

1239

Cov.:

AF XY:

0.0378

AC XY:

25603

AN XY:

676780

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.0225

Gnomad4 ASJ exome

AF:

0.0330

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.0424

Gnomad4 FIN exome

AF:

0.0312

Gnomad4 NFE exome

AF:

0.0333

Gnomad4 OTH exome

AF:

0.0424

GnomAD4 genome

AF:

0.0564

AC:

8595

AN:

152264

Hom.:

344

Cov.:

AF XY:

0.0553

AC XY:

4118

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0314

Gnomad4 ASJ

AF:

0.0337

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.0441

Gnomad4 FIN

AF:

0.0271

Gnomad4 NFE

AF:

0.0339

Gnomad4 OTH

AF:

0.0511

Alfa

AF:

0.0450

Hom.:

128

Bravo

AF:

0.0592

Asia WGS

AF:

0.0700

AC:

242

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

ZNF142-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 14, 2024

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.8

DANN

Benign

0.76

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over