NM_198088.3:c.467-3265G>C

Variant names:

• chr16-3227878-C-G
• rs12917706
• NM_198088.3:c.467-3265G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.549 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF200	NM_198088.3	MANE Select	c.467-3265G>C		intron	N/A	NP_932354.1	P98182-1
	ZNF200	NM_003454.4		c.467-3265G>C		intron	N/A	NP_003445.2
	ZNF200	NM_001145446.2		c.467-3268G>C		intron	N/A	NP_001138918.1	P98182-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF200	ENST00000414144.7	TSL:1 MANE Select	c.467-3265G>C		intron	N/A	ENSP00000405786.2	P98182-1
	ZNF200	ENST00000431561.7	TSL:1	c.467-3265G>C		intron	N/A	ENSP00000395723.3	P98182-1
	ZNF200	ENST00000396868.7	TSL:1	c.464-3265G>C		intron	N/A	ENSP00000380077.3	P98182-2

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

African (AFR) AF: 0.265 AC: 10960 AN: 41432

American (AMR) AF: 0.505 AC: 7702 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2927 AN: 5170

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4234 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29288 AN: 67948

Other (OTH) AF: 0.397 AC: 836 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		1.2
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: rs12917706; hg19: chr16-3277878;