20-2498552-A-G

Position:

• chr20-2498552-A-G

Variant summary

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

The NM_024325.6(ZNF343):​c.-150+2104T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,068 control chromosomes in the GnomAD database, including 12,176 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 0.39 (12176 hom., cov: 32)
• Consequence: ZNF343 NM_024325.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF343	NM_024325.6	c.-150+2104T>C		intron_variant		ENST00000278772.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF343	ENST00000278772.9	c.-150+2104T>C		intron_variant		2	NM_024325.6	P1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59502 AN: 151950 Hom.: 12169 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.391 AC: 59533 AN: 152068 Hom.: 12176 Cov.: 32 AF XY: 0.391 AC XY: 29062 AN XY: 74316

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.389

Alfa AF: 0.414 Hom.: 3119

Bravo AF: 0.377

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.45

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: rs1547063; hg19: chr20-2479198;