16-3230974-A-G

Position:

• chr16-3230974-A-G

Variant summary

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

The NM_198088.3(ZNF200):​c.466+1447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,178 control chromosomes in the GnomAD database, including 39,371 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 0.71 (39371 hom., cov: 32)
• Consequence: ZNF200 NM_198088.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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]

ZNF200 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF200	NM_198088.3	c.466+1447T>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.466+1447T>C		intron_variant		1	NM_198088.3	ENSP00000405786.2

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107521 AN: 152060 Hom.: 39309 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.707 AC: 107646 AN: 152178 Hom.: 39371 Cov.: 32 AF XY: 0.711 AC XY: 52916 AN XY: 74386

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.706

Alfa AF: 0.657 Hom.: 4273

Bravo AF: 0.728

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.38

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: rs401298; hg19: chr16-3280974;