NM_024325.6:c.-149-1941T>C

Variant names:

• chr20-2495985-A-G
• rs6083460
• NM_024325.6:c.-149-1941T>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.-149-1941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,070 control chromosomes in the GnomAD database, including 14,203 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 0.43 (14203 hom., cov: 32)
• Consequence: ZNF343 NM_024325.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF343	NM_024325.6	MANE Select	c.-149-1941T>C		intron	N/A	NP_077301.4
	ZNF343	NM_001282497.2		c.-149-1941T>C		intron	N/A	NP_001269426.1
	ZNF343	NM_001321801.2		c.-149-1941T>C		intron	N/A	NP_001308730.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF343	ENST00000278772.9	TSL:2 MANE Select	c.-149-1941T>C		intron	N/A	ENSP00000278772.4
	ZNF343	ENST00000445484.5	TSL:1	c.-259-461T>C		intron	N/A	ENSP00000399682.1
	ZNF343	ENST00000381253.5	TSL:1	c.-149-1941T>C		intron	N/A	ENSP00000370652.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65122 AN: 151952 Hom.: 14190 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.429 AC: 65176 AN: 152070 Hom.: 14203 Cov.: 32 AF XY: 0.427 AC XY: 31755 AN XY: 74330

African (AFR) AF: 0.404 AC: 16757 AN: 41490

American (AMR) AF: 0.358 AC: 5476 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1517 AN: 5168

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4814

European-Finnish (FIN) AF: 0.481 AC: 5073 AN: 10554

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

European-Non Finnish (NFE) AF: 0.465 AC: 31605 AN: 67980

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.449 Hom.: 26634

Bravo AF: 0.419

Asia WGS AF: 0.358 AC: 1244 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	1.4
DANN	Benign	0.13
PhyloP100		-1.7
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: rs6083460; hg19: chr20-2476631;