16-3227878-C-G

Position:

• chr16-3227878-C-G

Variant summary

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

The NM_198088.3(ZNF200):​c.467-3265G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,966 control chromosomes in the GnomAD database, including 12,350 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 0.39 (12350 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZNF200 NM_198088.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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 (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF200	NM_198088.3	c.467-3265G>C		intron_variant		ENST00000414144.7	NP_932354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF200	ENST00000414144.7	c.467-3265G>C		intron_variant		1	NM_198088.3	ENSP00000405786	P4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59840 AN: 151848 Hom.: 12332 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.394 AC: 59884 AN: 151966 Hom.: 12350 Cov.: 32 AF XY: 0.397 AC XY: 29509 AN XY: 74276

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.397

Alfa AF: 0.287 Hom.: 842

Bravo AF: 0.402

Asia WGS AF: 0.470 AC: 1632 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	6.6
DANN	Benign	0.68

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: rs12917706; hg19: chr16-3277878;