Variant chr19-52034081-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_014650.4(ZNF432):c.1598G>A(p.Arg533Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00887 in 1,614,160 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0079 ( 14 hom., cov: 33)

Exomes 𝑓: 0.0090 ( 84 hom. )

Consequence

ZNF432
NM_014650.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

ZNF432 (HGNC:20810): (zinc finger protein 432) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF432 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0055719614).

BP6

Variant 19-52034081-C-T is Benign according to our data. Variant chr19-52034081-C-T is described in ClinVar as [Benign]. Clinvar id is 777533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ZNF432	NM_014650.4 linkuse as main transcript	c.1598G>A	p.Arg533Gln	missense_variant	5/5	ENST00000221315.10
ZNF432	NM_001322284.2 linkuse as main transcript	c.1598G>A	p.Arg533Gln	missense_variant	5/5
ZNF432	NM_001322285.1 linkuse as main transcript	c.1598G>A	p.Arg533Gln	missense_variant	5/5
ZNF432	XM_024451806.2 linkuse as main transcript	c.1310G>A	p.Arg437Gln	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF432	ENST00000221315.10 linkuse as main transcript	c.1598G>A	p.Arg533Gln	missense_variant	5/5	1	NM_014650.4	P1
ZNF432	ENST00000594154.5 linkuse as main transcript	c.1598G>A	p.Arg533Gln	missense_variant	5/5	1		P1

Frequencies

GnomAD3 genomes

AF:

0.00792

AC:

1206

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00191

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.0201

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00923

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00802

AC:

2016

AN:

251364

Hom.:

AF XY:

0.00801

AC XY:

1088

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00757

Gnomad ASJ exome

AF:

0.00109

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.0192

Gnomad NFE exome

AF:

0.0105

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.00896

AC:

13104

AN:

1461834

Hom.:

Cov.:

AF XY:

0.00888

AC XY:

6458

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00830

Gnomad4 ASJ exome

AF:

0.00134

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000800

Gnomad4 FIN exome

AF:

0.0201

Gnomad4 NFE exome

AF:

0.00979

Gnomad4 OTH exome

AF:

0.00902

GnomAD4 genome

AF:

0.00792

AC:

1206

AN:

152326

Hom.:

Cov.:

AF XY:

0.00858

AC XY:

639

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00190

Gnomad4 AMR

AF:

0.0160

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00103

Gnomad4 FIN

AF:

0.0201

Gnomad4 NFE

AF:

0.00923

Gnomad4 OTH

AF:

0.00992

Alfa

AF:

0.00890

Hom.:

Bravo

AF:

0.00771

TwinsUK

AF:

0.0116

AC:

ALSPAC

AF:

0.0125

AC:

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.0119

AC:

102

ExAC

AF:

0.00744

AC:

903

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0119

EpiControl

AF:

0.0110

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	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.10

T;T

Eigen

Benign

0.061

Eigen_PC

Benign

-0.071

FATHMM_MKL

Benign

0.0013

LIST_S2

Benign

0.28

.;T

MetaRNN

Benign

0.0056

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

L;L

MutationTaster

Benign

1.0

PrimateAI

Benign

0.41

PROVEAN

Uncertain

-2.9

.;D

REVEL

Benign

0.12

Sift

Uncertain

0.013

.;D

Sift4G

Uncertain

0.027

D;D

Polyphen

0.99

D;D

Vest4

0.18

MVP

0.30

MPC

0.31

ClinPred

0.036

GERP RS

2.8

Varity_R

0.28

gMVP

0.066

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