Variant chr20-2483284-G-A 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.1677C>T(p.Ser559=) 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 0.0023 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00012 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

ZNF343
NM_024325.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.54

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 20-2483284-G-A is Benign according to our data. Variant chr20-2483284-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3025474.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.54 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF343	NM_024325.6 linkuse as main transcript	c.1677C>T	p.Ser559=	synonymous_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.1677C>T	p.Ser559=	synonymous_variant	6/6	2	NM_024325.6	P1	Q6P1L6-1
ZNF343	ENST00000612935.4 linkuse as main transcript	c.1800C>T	p.Ser600=	synonymous_variant	8/8	5
ZNF343	ENST00000617391.4 linkuse as main transcript	c.1407C>T	p.Ser469=	synonymous_variant	4/4	4			Q6P1L6-2
ZNF343	ENST00000465019.1 linkuse as main transcript	n.1705C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

289

AN:

124470

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00392

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.000327

Gnomad EAS

AF:

0.00423

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.00486

Gnomad MID

AF:

0.0313

Gnomad NFE

AF:

0.00102

Gnomad OTH

AF:

0.00118

GnomAD3 exomes

AF:

0.0000721

AC:

AN:

222016

Hom.:

AF XY:

0.0000743

AC XY:

AN XY:

121154

show subpopulations

Gnomad AFR exome

AF:

0.000365

Gnomad AMR exome

AF:

0.000108

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000696

Gnomad SAS exome

AF:

0.000150

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000289

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000123

AC:

172

AN:

1401754

Hom.:

Cov.:

AF XY:

0.000126

AC XY:

AN XY:

697634

show subpopulations

Gnomad4 AFR exome

AF:

0.000361

Gnomad4 AMR exome

AF:

0.00165

Gnomad4 ASJ exome

AF:

0.0000418

Gnomad4 EAS exome

AF:

0.000311

Gnomad4 SAS exome

AF:

0.000284

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000398

Gnomad4 OTH exome

AF:

0.000371

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00233

AC:

290

AN:

124542

Hom.:

Cov.:

AF XY:

0.00238

AC XY:

145

AN XY:

61036

show subpopulations

Gnomad4 AFR

AF:

0.00397

Gnomad4 AMR

AF:

0.00192

Gnomad4 ASJ

AF:

0.000327

Gnomad4 EAS

AF:

0.00399

Gnomad4 SAS

AF:

0.00418

Gnomad4 FIN

AF:

0.00486

Gnomad4 NFE

AF:

0.00102

Gnomad4 OTH

AF:

0.00118

Alfa

AF:

0.00516

Hom.:

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

Feb 01, 2024

ZNF343: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.4

DANN

Benign

0.81

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