Variant chr20-2483536-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_024325.6(ZNF343):c.1425T>C(p.Ser475Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0048 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000072 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF343
NM_024325.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.499

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:

ENSG00000256566 (HGNC:):

ENSG00000256566 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 20-2483536-A-G is Benign according to our data. Variant chr20-2483536-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3025039.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.499 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF343	NM_024325.6 link	c.1425T>C	p.Ser475Ser	synonymous_variant	6/6	ENST00000278772.9	NP_077301.4	Q6P1L6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF343	ENST00000278772.9 link	c.1425T>C	p.Ser475Ser	synonymous_variant	6/6	2	NM_024325.6	ENSP00000278772.4		Q6P1L6-1
ENSG00000256566	ENST00000461548.1 link	n.304+9163T>C		intron_variant		5		ENSP00000456213.1		F5H5K5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

594

AN:

125806

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00639

Gnomad AMI

AF:

0.00956

Gnomad AMR

AF:

0.00386

Gnomad ASJ

AF:

0.00161

Gnomad EAS

AF:

0.00474

Gnomad SAS

AF:

0.00574

Gnomad FIN

AF:

0.00810

Gnomad MID

AF:

0.0150

Gnomad NFE

AF:

0.00362

Gnomad OTH

AF:

0.00168

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000719

AC:

105

AN:

1460360

Hom.:

Cov.:

AF XY:

0.0000977

AC XY:

AN XY:

726542

show subpopulations

Gnomad4 AFR exome

AF:

0.000150

Gnomad4 AMR exome

AF:

0.000226

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.000545

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.0000306

Gnomad4 OTH exome

AF:

0.0000663

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00476

AC:

599

AN:

125906

Hom.:

Cov.:

AF XY:

0.00484

AC XY:

297

AN XY:

61422

show subpopulations

Gnomad4 AFR

AF:

0.00640

Gnomad4 AMR

AF:

0.00394

Gnomad4 ASJ

AF:

0.00161

Gnomad4 EAS

AF:

0.00476

Gnomad4 SAS

AF:

0.00654

Gnomad4 FIN

AF:

0.00810

Gnomad4 NFE

AF:

0.00362

Gnomad4 OTH

AF:

0.00167

Alfa

AF:

0.00514

Hom.:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

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, 2024

ZNF343: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

DANN

Benign

0.61

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