rs1547063

Variant names:

• chr20-2498552-A-G
• rs1547063
• NM_024325.6:c.-150+2104T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000256566 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024325.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF343	NM_024325.6	MANE Select	c.-150+2104T>C		intron	N/A	NP_077301.4
	ZNF343	NM_001282497.2		c.-150+2104T>C		intron	N/A	NP_001269426.1	A0A087WZQ2
	ZNF343	NM_001321801.2		c.-150+2104T>C		intron	N/A	NP_001308730.1	A0A087WZQ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF343	ENST00000278772.9	TSL:2 MANE Select	c.-150+2104T>C		intron	N/A	ENSP00000278772.4	Q6P1L6-1
	ZNF343	ENST00000445484.5	TSL:1	c.-260+2104T>C		intron	N/A	ENSP00000399682.1	A0A0A0MSR0
	ZNF343	ENST00000381253.5	TSL:1	c.-150+2104T>C		intron	N/A	ENSP00000370652.1	Q6P1L6-3

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

African (AFR) AF: 0.294 AC: 12213 AN: 41488

American (AMR) AF: 0.329 AC: 5024 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1561 AN: 5172

South Asian (SAS) AF: 0.373 AC: 1801 AN: 4824

European-Finnish (FIN) AF: 0.483 AC: 5098 AN: 10554

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30992 AN: 67962

Other (OTH) AF: 0.389 AC: 820 AN: 2110

Alfa AF: 0.411 Hom.: 5355

Bravo AF: 0.377

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1547063; hg19: chr20-2479198;