rs6083461

chr20-2496132-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024325.6(ZNF343):c.-149-2088T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,038 control chromosomes in the GnomAD database, including 13,585 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13585 hom., cov: 32)
• Consequence: ZNF343 NM_024325.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF343	NM_024325.6	c.-149-2088T>A		intron_variant		ENST00000278772.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF343	ENST00000278772.9	c.-149-2088T>A		intron_variant		2	NM_024325.6	P1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63578 AN: 151920 Hom.: 13574 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.418 AC: 63625 AN: 152038 Hom.: 13585 Cov.: 32 AF XY: 0.417 AC XY: 30994 AN XY: 74314

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.418

Alfa AF: 0.450 Hom.: 1957

Bravo AF: 0.408

Asia WGS AF: 0.357 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.66

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: rs6083461; hg19: chr20-2476778;