Variant 20-2483588-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_024325.6(ZNF343):c.1373C>T(p.Thr458Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00565 in 1,612,832 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0059 ( 28 hom. )

Consequence

ZNF343
NM_024325.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00100

Variant links:

Genes affected

ZNF343 (HGNC:16017): (zinc finger protein 343) Enables sequence-specific double-stranded 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]

ZNF343 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=0.010852188).

BP6

Variant 20-2483588-G-A is Benign according to our data. Variant chr20-2483588-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2652148.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 28 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF343	NM_024325.6 linkuse as main transcript	c.1373C>T	p.Thr458Met	missense_variant	6/6	ENST00000278772.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF343	ENST00000278772.9 linkuse as main transcript	c.1373C>T	p.Thr458Met	missense_variant	6/6	2	NM_024325.6	P1	Q6P1L6-1
ZNF343	ENST00000612935.4 linkuse as main transcript	c.1496C>T	p.Thr499Met	missense_variant	8/8	5
ZNF343	ENST00000617391.4 linkuse as main transcript	c.1103C>T	p.Thr368Met	missense_variant	4/4	4			Q6P1L6-2
ZNF343	ENST00000465019.1 linkuse as main transcript	n.1401C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.00366

AC:

552

AN:

150886

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00132

Gnomad AMI

AF:

0.0352

Gnomad AMR

AF:

0.00185

Gnomad ASJ

AF:

0.00722

Gnomad EAS

AF:

0.000390

Gnomad SAS

AF:

0.00230

Gnomad FIN

AF:

0.0000966

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00579

Gnomad OTH

AF:

0.00290

GnomAD3 exomes

AF:

0.00359

AC:

902

AN:

251446

Hom.:

AF XY:

0.00372

AC XY:

505

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00159

Gnomad ASJ exome

AF:

0.00744

Gnomad EAS exome

AF:

0.000217

Gnomad SAS exome

AF:

0.00242

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00576

Gnomad OTH exome

AF:

0.00293

GnomAD4 exome

AF:

0.00586

AC:

8565

AN:

1461834

Hom.:

Cov.:

AF XY:

0.00565

AC XY:

4112

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.000836

Gnomad4 AMR exome

AF:

0.00186

Gnomad4 ASJ exome

AF:

0.00662

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00260

Gnomad4 FIN exome

AF:

0.000580

Gnomad4 NFE exome

AF:

0.00691

Gnomad4 OTH exome

AF:

0.00540

GnomAD4 genome

AF:

0.00366

AC:

552

AN:

150998

Hom.:

Cov.:

AF XY:

0.00350

AC XY:

258

AN XY:

73728

show subpopulations

Gnomad4 AFR

AF:

0.00132

Gnomad4 AMR

AF:

0.00185

Gnomad4 ASJ

AF:

0.00722

Gnomad4 EAS

AF:

0.000391

Gnomad4 SAS

AF:

0.00230

Gnomad4 FIN

AF:

0.0000966

Gnomad4 NFE

AF:

0.00579

Gnomad4 OTH

AF:

0.00287

Alfa

AF:

0.00530

Hom.:

Bravo

AF:

0.00367

TwinsUK

AF:

0.00755

AC:

ALSPAC

AF:

0.00649

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00477

AC:

ExAC

AF:

0.00332

AC:

403

EpiCase

AF:

0.00529

EpiControl

AF:

0.00569

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

Jul 01, 2022

ZNF343: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.064

T;.;.

Eigen

Benign

-0.37

Eigen_PC

Benign

-0.60

FATHMM_MKL

Benign

0.061

LIST_S2

Benign

0.24

T;T;T

M_CAP

Benign

0.011

MetaRNN

Benign

0.011

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.4

M;.;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-4.3

D;.;.

REVEL

Benign

0.022

Sift

Uncertain

0.010

D;.;.

Sift4G

Uncertain

0.018

D;D;D

Polyphen

1.0

D;.;.

Vest4

0.066

MVP

0.42

MPC

0.24

ClinPred

0.058

GERP RS

1.3

Varity_R

0.056

gMVP

0.021

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