20-2482946-T-C

Position:

• chr20-2482946-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZNF343	NM_024325.6	c.*215A>G		3_prime_UTR_variant	6/6	ENST00000278772.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF343	ENST00000278772.9	c.*215A>G		3_prime_UTR_variant	6/6	2	NM_024325.6	P1
ZNF343	ENST00000612935.4	c.*215A>G		3_prime_UTR_variant	8/8	5
ZNF343	ENST00000617391.4	c.*215A>G		3_prime_UTR_variant	4/4	4
ZNF343	ENST00000465019.1	n.2043A>G		non_coding_transcript_exon_variant	2/2	2

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

Gnomad4 AFR exome AF: 0.459

Gnomad4 AMR exome AF: 0.738

Gnomad4 ASJ exome AF: 0.730

Gnomad4 EAS exome AF: 0.740

Gnomad4 SAS exome AF: 0.647

Gnomad4 FIN exome AF: 0.692

Gnomad4 NFE exome AF: 0.786

Gnomad4 OTH exome AF: 0.735

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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.706

Alfa AF: 0.712 Hom.: 9553

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs3746687; hg19: chr20-2463592;