Variant chr14-104801767-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001137601.3(ZBTB42):c.570G>A(p.Leu190=) variant causes a synonymous change. The variant allele was found at a frequency of 0.274 in 1,548,706 control chromosomes in the GnomAD database, including 59,318 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6127 hom., cov: 34)

Exomes 𝑓: 0.27 ( 53191 hom. )

Consequence

ZBTB42
NM_001137601.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.02

Variant links:

Genes affected

ZBTB42 (HGNC:32550): (zinc finger and BTB domain containing 42) The protein encoded by this gene is a member of the C2H2 zinc finger protein family. This protein is predicted to have a pox virus and zinc finger (POZ) domain at the N-terminus and four zinc finger domains at the C-terminus. In human and mouse, the protein localizes to the nuclei of skeletal muscle cells. Knockdown of this gene in zebrafish results in abnormal skeletal muscle development and myofibrillar disorganization. A novel homozygous variant of the human gene has been associated with lethal congenital contracture syndrome, an autosomal recessive disorder that results in muscle wasting. [provided by RefSeq, Mar 2015]

ZBTB42 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 14-104801767-G-A is Benign according to our data. Variant chr14-104801767-G-A is described in ClinVar as [Benign]. Clinvar id is 1260467.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB42	NM_001137601.3 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	1/1	ENST00000342537.8
ZBTB42	NM_001370342.1 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB42	ENST00000342537.8 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	1/1		NM_001137601.3	P1
ZBTB42	ENST00000555360.1 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	2/2	1		P1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42125

AN:

152046

Hom.:

6116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.265

GnomAD3 exomes

AF:

0.242

AC:

36710

AN:

151526

Hom.:

4691

AF XY:

0.242

AC XY:

19521

AN XY:

80710

show subpopulations

Gnomad AFR exome

AF:

0.320

Gnomad AMR exome

AF:

0.197

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.113

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.282

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.274

AC:

382272

AN:

1396542

Hom.:

53191

Cov.:

AF XY:

0.271

AC XY:

186906

AN XY:

688572

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.208

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.286

Gnomad4 OTH exome

AF:

0.259

GnomAD4 genome

AF:

0.277

AC:

42172

AN:

152164

Hom.:

6127

Cov.:

AF XY:

0.275

AC XY:

20428

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.286

Gnomad4 OTH

AF:

0.266

Alfa

AF:

0.247

Hom.:

1967

Bravo

AF:

0.276

Asia WGS

AF:

0.135

AC:

466

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

9.5

DANN

Benign

0.81

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