chr20-2483536-A-G

Position:

• chr20-2483536-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_024325.6(ZNF343):​c.1425T>C​(p.Ser475=) 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.499

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]

ACMG classification

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	UniProt
ZNF343	NM_024325.6	c.1425T>C	p.Ser475=	synonymous_variant	6/6	ENST00000278772.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF343	ENST00000278772.9	c.1425T>C	p.Ser475=	synonymous_variant	6/6	2	NM_024325.6	P1
ZNF343	ENST00000612935.4	c.1548T>C	p.Ser516=	synonymous_variant	8/8	5
ZNF343	ENST00000617391.4	c.1155T>C	p.Ser385=	synonymous_variant	4/4	4
ZNF343	ENST00000465019.1	n.1453T>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 594 AN: 125806 Hom.: 0 Cov.: 32 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.: 0 Cov.: 32 AF XY: 0.0000977 AC XY: 71 AN XY: 726542

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.: 0 Cov.: 32 AF XY: 0.00484 AC XY: 297 AN XY: 61422

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.: 0

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

Other links and lift over

dbSNP: rs528685225; hg19: chr20-2464182; COSMIC: COSV53854022; COSMIC: COSV53854022;