chr20-2491109-T-C

Variant names:

• chr20-2491109-T-C
• rs6076199
• NM_024325.6:c.304+1590A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024325.6(ZNF343):​c.304+1590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,046 control chromosomes in the GnomAD database, including 11,449 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 0.38 (11449 hom., cov: 32)
• Consequence: ZNF343 NM_024325.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15
• Publications: 1 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=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF343	NM_024325.6	c.304+1590A>G		intron_variant	Intron 5 of 5	ENST00000278772.9	NP_077301.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF343	ENST00000278772.9	c.304+1590A>G		intron_variant	Intron 5 of 5	2	NM_024325.6	ENSP00000278772.4
ENSG00000256566	ENST00000461548.1	n.304+1590A>G		intron_variant	Intron 5 of 6	5		ENSP00000456213.1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57016 AN: 151926 Hom.: 11443 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.375 AC: 57035 AN: 152046 Hom.: 11449 Cov.: 32 AF XY: 0.374 AC XY: 27806 AN XY: 74306

African (AFR) AF: 0.241 AC: 10009 AN: 41500

American (AMR) AF: 0.330 AC: 5044 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5170

South Asian (SAS) AF: 0.396 AC: 1911 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4876 AN: 10524

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30952 AN: 67970

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.434 Hom.: 25128

Bravo AF: 0.359

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		2.1
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: rs6076199; hg19: chr20-2471755;