16-3232275-C-A

Variant names:

• chr16-3232275-C-A
• rs9927763
• NM_198088.3:c.466+146G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198088.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF200	NM_198088.3	MANE Select	c.466+146G>T		intron	N/A	NP_932354.1
	ZNF200	NM_003454.4		c.466+146G>T		intron	N/A	NP_003445.2
	ZNF200	NM_001145446.2		c.466+146G>T		intron	N/A	NP_001138918.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF200	ENST00000414144.7	TSL:1 MANE Select	c.466+146G>T		intron	N/A	ENSP00000405786.2
	ZNF200	ENST00000431561.7	TSL:1	c.466+146G>T		intron	N/A	ENSP00000395723.3
	ZNF200	ENST00000396868.7	TSL:1	c.463+146G>T		intron	N/A	ENSP00000380077.3

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

African (AFR) AF: 0.219 AC: 4145 AN: 18960

American (AMR) AF: 0.0789 AC: 1783 AN: 22594

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 1702 AN: 14992

East Asian (EAS) AF: 0.0314 AC: 1001 AN: 31904

South Asian (SAS) AF: 0.284 AC: 15251 AN: 53766

European-Finnish (FIN) AF: 0.0294 AC: 971 AN: 33014

Middle Eastern (MID) AF: 0.118 AC: 297 AN: 2516

European-Non Finnish (NFE) AF: 0.0561 AC: 35285 AN: 629436

Other (OTH) AF: 0.0825 AC: 3066 AN: 37154

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

African (AFR) AF: 0.223 AC: 9245 AN: 41428

American (AMR) AF: 0.0761 AC: 1163 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3472

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5182

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4818

European-Finnish (FIN) AF: 0.0247 AC: 262 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3961 AN: 68016

Other (OTH) AF: 0.106 AC: 224 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.20
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: rs9927763; hg19: chr16-3282275; COSMIC: COSV107504258; COSMIC: COSV107504258;