NM_024325.6:c.*215A>G

Variant names:

• chr20-2482946-T-C
• rs3746687
• NM_024325.6:c.*215A>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.*215A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 581,924 control chromosomes in the GnomAD database, including 158,630 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 0.68 (36472 hom., cov: 31)
  • Exomes 𝑓: 0.75 (122158 hom.)
• Consequence: ZNF343 NM_024325.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF343	NM_024325.6	c.*215A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000278772.9	NP_077301.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF343	ENST00000278772.9	c.*215A>G		3_prime_UTR_variant	Exon 6 of 6	2	NM_024325.6	ENSP00000278772.4
ENSG00000256566	ENST00000461548.1	n.304+9753A>G		intron_variant	Intron 5 of 6	5		ENSP00000456213.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102904 AN: 151900 Hom.: 36460 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.709

GnomAD4 exome AF: 0.749 AC: 322116 AN: 429906 Hom.: 122158 Cov.: 5 AF XY: 0.748 AC XY: 167088 AN XY: 223520

African (AFR) AF: 0.459 AC: 5632 AN: 12282

American (AMR) AF: 0.738 AC: 11984 AN: 16248

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 9494 AN: 13006

East Asian (EAS) AF: 0.740 AC: 22216 AN: 30012

South Asian (SAS) AF: 0.647 AC: 22797 AN: 35212

European-Finnish (FIN) AF: 0.692 AC: 19407 AN: 28060

Middle Eastern (MID) AF: 0.744 AC: 1398 AN: 1880

European-Non Finnish (NFE) AF: 0.786 AC: 210925 AN: 268374

Other (OTH) AF: 0.735 AC: 18263 AN: 24832

GnomAD4 genome AF: 0.677 AC: 102952 AN: 152018 Hom.: 36472 Cov.: 31 AF XY: 0.675 AC XY: 50130 AN XY: 74298

African (AFR) AF: 0.459 AC: 18999 AN: 41428

American (AMR) AF: 0.745 AC: 11395 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2536 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3777 AN: 5176

South Asian (SAS) AF: 0.639 AC: 3074 AN: 4812

European-Finnish (FIN) AF: 0.689 AC: 7277 AN: 10562

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53452 AN: 67968

Other (OTH) AF: 0.706 AC: 1487 AN: 2106

Alfa AF: 0.707 Hom.: 9628

Bravo AF: 0.673

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.60
PhyloP100		-2.2
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: rs3746687; hg19: chr20-2463592;