Variant 19-57839084-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_001376223.1(ZNF587B):c.98G>A(p.Ser33Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000787 in 1,614,098 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 4 hom., cov: 31)

Exomes 𝑓: 0.00052 ( 4 hom. )

Consequence

ZNF587B
NM_001376223.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.787

Variant links:

Genes affected

ZNF587B (HGNC:37142): (zinc finger protein 587B) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF587B links:

ENSG00000268750 (HGNC:):

ENSG00000268750 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=0.0061003864).

BP6

Variant 19-57839084-G-A is Benign according to our data. Variant chr19-57839084-G-A is described in ClinVar as [Benign]. Clinvar id is 713407.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF587B	NM_001376223.1 linkuse as main transcript	c.98G>A	p.Ser33Asn	missense_variant	2/3	ENST00000594901.2	NP_001363152.1
ZNF587B	NM_001204818.2 linkuse as main transcript	c.98G>A	p.Ser33Asn	missense_variant	2/4		NP_001191747.1	E7ETH6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZNF587B	ENST00000594901.2 linkuse as main transcript	c.98G>A	p.Ser33Asn	missense_variant	2/3	4	NM_001376223.1	ENSP00000469623.1	M0QY62
ZNF587B	ENST00000442832.8 linkuse as main transcript	c.98G>A	p.Ser33Asn	missense_variant	2/4	2		ENSP00000392410.2	E7ETH6
ENSG00000268750	ENST00000593873.6 linkuse as main transcript	c.33+19139G>A		intron_variant		4		ENSP00000469133.2	M0QXF5

Frequencies

GnomAD3 genomes

AF:

0.00333

AC:

506

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00127

AC:

319

AN:

251442

Hom.:

AF XY:

0.00107

AC XY:

146

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00186

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.000114

Gnomad OTH exome

AF:

0.000815

GnomAD4 exome

AF:

0.000523

AC:

765

AN:

1461836

Hom.:

Cov.:

AF XY:

0.000499

AC XY:

363

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.0123

Gnomad4 AMR exome

AF:

0.00110

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00180

Gnomad4 FIN exome

AF:

0.000225

Gnomad4 NFE exome

AF:

0.0000639

Gnomad4 OTH exome

AF:

0.000993

GnomAD4 genome

AF:

0.00332

AC:

506

AN:

152262

Hom.:

Cov.:

AF XY:

0.00338

AC XY:

252

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0110

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00184

Hom.:

Bravo

AF:

0.00399

ExAC

AF:

0.00146

AC:

177

EpiCase

AF:

0.000436

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.9

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0049

T;.

Eigen

Benign

-0.78

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.00085

LIST_S2

Benign

0.069

T;T

MetaRNN

Benign

0.0061

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-0.18

N;.

PROVEAN

Benign

-0.71

N;.

REVEL

Benign

0.096

Sift

Uncertain

0.024

D;.

Sift4G

Uncertain

0.060

T;T

Polyphen

0.59

P;.

Vest4

0.10

MVP

0.12

MPC

1.0

ClinPred

0.030

GERP RS

1.0

Varity_R

0.034

gMVP

0.045

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