16-3232605-T-C

Variant summary

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

The NM_198088.3(ZNF200):c.340-58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,596,994 control chromosomes in the GnomAD database, including 183,865 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 0.44 (14939 hom., cov: 32)
  • Exomes 𝑓: 0.48 (168926 hom.)
• Consequence: ZNF200 NM_198088.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF200	NM_198088.3	c.340-58A>G		intron_variant		ENST00000414144.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF200	ENST00000414144.7	c.340-58A>G		intron_variant		1	NM_198088.3	P4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66080 AN: 151816 Hom.: 14923 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.480 AC: 694247 AN: 1445060 Hom.: 168926 Cov.: 33 AF XY: 0.478 AC XY: 343313 AN XY: 718812

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.645

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.582

Gnomad4 SAS exome AF: 0.422

Gnomad4 FIN exome AF: 0.489

Gnomad4 NFE exome AF: 0.482

Gnomad4 OTH exome AF: 0.468

GnomAD4 genome AF: 0.435 AC: 66130 AN: 151934 Hom.: 14939 Cov.: 32 AF XY: 0.438 AC XY: 32538 AN XY: 74254

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.435

Alfa AF: 0.466 Hom.: 17504

Bravo AF: 0.440

Asia WGS AF: 0.482 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.2
Dann	Benign	0.49

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: rs2075852; hg19: chr16-3282605;