rs6083461

Variant names:

• chr20-2496132-A-T
• rs6083461
• NM_024325.6:c.-149-2088T>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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.-149-2088T>A		intron	N/A	NP_077301.4
	ZNF343	NM_001282497.2		c.-149-2088T>A		intron	N/A	NP_001269426.1	A0A087WZQ2
	ZNF343	NM_001321801.2		c.-149-2088T>A		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.-149-2088T>A		intron	N/A	ENSP00000278772.4	Q6P1L6-1
	ZNF343	ENST00000445484.5	TSL:1	c.-259-608T>A		intron	N/A	ENSP00000399682.1	A0A0A0MSR0
	ZNF343	ENST00000381253.5	TSL:1	c.-149-2088T>A		intron	N/A	ENSP00000370652.1	Q6P1L6-3

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

African (AFR) AF: 0.369 AC: 15316 AN: 41460

American (AMR) AF: 0.354 AC: 5412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5168

South Asian (SAS) AF: 0.380 AC: 1836 AN: 4832

European-Finnish (FIN) AF: 0.481 AC: 5069 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31581 AN: 67962

Other (OTH) AF: 0.418 AC: 882 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.51
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: rs6083461; hg19: chr20-2476778;