Variant 19-34931868-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_194325.3(ZNF30):c.35G>A(p.Gly12Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00617 in 1,612,202 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 39 hom. )

Consequence

ZNF30
NM_194325.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00200

Variant links:

Genes affected

ZNF30 (HGNC:13090): (zinc finger protein 30) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF30 links:

ZNF30 (HGNC:):

ZNF30 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0046146214).

BP6

Variant 19-34931868-G-A is Benign according to our data. Variant chr19-34931868-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2649709.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF30	NM_194325.3 linkuse as main transcript	c.35G>A	p.Gly12Glu	missense_variant	3/5	ENST00000601142.2	NP_919306.2	P17039-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF30	ENST00000601142.2 linkuse as main transcript	c.35G>A	p.Gly12Glu	missense_variant	3/5	2	NM_194325.3	ENSP00000469954.1		P17039-1

Frequencies

GnomAD3 genomes

AF:

0.00461

AC:

702

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00783

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00441

AC:

1093

AN:

247912

Hom.:

AF XY:

0.00444

AC XY:

597

AN XY:

134552

show subpopulations

Gnomad AFR exome

AF:

0.00143

Gnomad AMR exome

AF:

0.00220

Gnomad ASJ exome

AF:

0.0121

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000893

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00697

Gnomad OTH exome

AF:

0.00583

GnomAD4 exome

AF:

0.00634

AC:

9250

AN:

1459886

Hom.:

Cov.:

AF XY:

0.00632

AC XY:

4587

AN XY:

726210

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000967

Gnomad4 FIN exome

AF:

0.00225

Gnomad4 NFE exome

AF:

0.00742

Gnomad4 OTH exome

AF:

0.00565

GnomAD4 genome

AF:

0.00461

AC:

702

AN:

152316

Hom.:

Cov.:

AF XY:

0.00435

AC XY:

324

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00783

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00692

Hom.:

Bravo

AF:

0.00430

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.00623

AC:

ESP6500AA

AF:

0.000471

AC:

ESP6500EA

AF:

0.00798

AC:

ExAC

AF:

0.00446

AC:

541

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00616

EpiControl

AF:

0.00684

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

ZNF30: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.4

DANN

Benign

0.73

DEOGEN2

Benign

0.013

.;.;.;.;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.15

.;T;T;T;T

M_CAP

Benign

0.0026

MetaRNN

Benign

0.0046

T;T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.53

N;N;.;N;N

PrimateAI

Uncertain

0.49

PROVEAN

Benign

0.66

N;N;.;.;.

REVEL

Benign

0.061

Sift

Benign

0.44

T;T;.;.;.

Sift4G

Benign

0.45

T;T;T;T;T

Polyphen

0.0020

B;B;.;.;B

Vest4

0.13

MVP

0.23

MPC

0.047

ClinPred

0.0025

GERP RS

-0.74

Varity_R

0.096

gMVP

0.080

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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