rs9927763

Positions:

• chr16-3232275-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198088.3(ZNF200):​c.466+146G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 996,442 control chromosomes in the GnomAD database, including 5,745 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 0.11 (1473 hom., cov: 32)
  • Exomes 𝑓: 0.075 (4272 hom.)
• Consequence: ZNF200 NM_198088.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

ZNF200 (HGNC:12993): (zinc finger protein 200) Predicted to enable metal ion binding activity. 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF200	NM_198088.3	c.466+146G>T		intron_variant		ENST00000414144.7	NP_932354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF200	ENST00000414144.7	c.466+146G>T		intron_variant		1	NM_198088.3	ENSP00000405786	P4

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16893 AN: 151988 Hom.: 1470 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.102

GnomAD4 exome AF: 0.0752 AC: 63501 AN: 844336 Hom.: 4272 AF XY: 0.0823 AC XY: 35207 AN XY: 427546

Gnomad4 AFR exome AF: 0.219

Gnomad4 AMR exome AF: 0.0789

Gnomad4 ASJ exome AF: 0.114

Gnomad4 EAS exome AF: 0.0314

Gnomad4 SAS exome AF: 0.284

Gnomad4 FIN exome AF: 0.0294

Gnomad4 NFE exome AF: 0.0561

Gnomad4 OTH exome AF: 0.0825

GnomAD4 genome AF: 0.111 AC: 16918 AN: 152106 Hom.: 1473 Cov.: 32 AF XY: 0.111 AC XY: 8255 AN XY: 74382

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.0247

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0852 Hom.: 148

Bravo AF: 0.114

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.40

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: rs9927763; hg19: chr16-3282275;