Variant chr19-56384127-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001320371.4(ZNF582):c.1290G>A(p.Lys430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,612,336 control chromosomes in the GnomAD database, including 15,257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1314 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13943 hom. )

Consequence

ZNF582
NM_001320371.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.519

Variant links:

Genes affected

ZNF582 (HGNC:26421): (zinc finger protein 582) The protein encoded by this gene is a zing finger protein and putative transcription factor that is highly methylated in cervical cancers. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ZNF582 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 19-56384127-C-T is Benign according to our data. Variant chr19-56384127-C-T is described in ClinVar as [Benign]. Clinvar id is 3058896.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.519 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ZNF582	NM_001320371.4 linkuse as main transcript	c.1290G>A	p.Lys430=	synonymous_variant	5/5	ENST00000586929.6	NP_001307300.2
ZNF582	NM_144690.3 linkuse as main transcript	c.1290G>A	p.Lys430=	synonymous_variant	5/5		NP_653291.1
ZNF582	XR_007066621.1 linkuse as main transcript	n.1463G>A		non_coding_transcript_exon_variant	5/6
ZNF582	XR_430188.4 linkuse as main transcript	n.1685G>A		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ZNF582	ENST00000586929.6 linkuse as main transcript	c.1290G>A	p.Lys430=	synonymous_variant	5/5	1	NM_001320371.4	ENSP00000465619	P1
ZNF582	ENST00000301310.8 linkuse as main transcript	c.1290G>A	p.Lys430=	synonymous_variant	5/5	1		ENSP00000301310	P1
ZNF582	ENST00000589143.5 linkuse as main transcript	c.232+5874G>A		intron_variant		5		ENSP00000468679
ZNF582	ENST00000589895.2 linkuse as main transcript	c.232+5874G>A		intron_variant		2		ENSP00000465639

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19264

AN:

152032

Hom.:

1310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.146

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.127

GnomAD3 exomes

AF:

0.152

AC:

37867

AN:

249788

Hom.:

3306

AF XY:

0.151

AC XY:

20410

AN XY:

135022

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.153

Gnomad EAS exome

AF:

0.308

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.127

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.133

AC:

194605

AN:

1460186

Hom.:

13943

Cov.:

AF XY:

0.135

AC XY:

97701

AN XY:

726372

show subpopulations

Gnomad4 AFR exome

AF:

0.0981

Gnomad4 AMR exome

AF:

0.157

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.142

GnomAD4 genome

AF:

0.127

AC:

19299

AN:

152150

Hom.:

1314

Cov.:

AF XY:

0.128

AC XY:

9546

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.146

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.124

Hom.:

689

Bravo

AF:

0.125

Asia WGS

AF:

0.219

AC:

761

AN:

3478

EpiCase

AF:

0.127

EpiControl

AF:

0.131

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZNF582-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

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

-0.60

CADD

Benign

5.2

DANN

Benign

0.80

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