rs728534

chr2-184937190-A-Gchr2-184937190-A-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_194250.2(ZNF804A):c.1794A>G(p.Lys598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,595,064 control chromosomes in the GnomAD database, including 33,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (2259 hom., cov: 33)
  • Exomes 𝑓: 0.20 (30930 hom.)
• Consequence: ZNF804A NM_194250.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.00

Genes affected

ZNF804A (HGNC:21711): (zinc finger protein 804A) The protein encoded by this gene is a zinc finger binding protein. Polymorphisms in this gene, especially rs1344706, are thought to confer increased susceptibility to schizophrenia, bipolar disorder, and heroin addiciton. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 2-184937190-A-G is Benign according to our data. Variant chr2-184937190-A-G is described in ClinVar as [Benign]. Clinvar id is 3060253.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804A	NM_194250.2	c.1794A>G	p.Lys598=	synonymous_variant	4/4	ENST00000302277.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804A	ENST00000302277.7	c.1794A>G	p.Lys598=	synonymous_variant	4/4	1	NM_194250.2	P1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23262 AN: 152064 Hom.: 2256 Cov.: 33

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.173

GnomAD3 exomes AF: 0.197 AC: 45328 AN: 230060 Hom.: 5072 AF XY: 0.206 AC XY: 25895 AN XY: 125492

Gnomad AFR exome AF: 0.0343

Gnomad AMR exome AF: 0.107

Gnomad ASJ exome AF: 0.207

Gnomad EAS exome AF: 0.245

Gnomad SAS exome AF: 0.280

Gnomad FIN exome AF: 0.232

Gnomad NFE exome AF: 0.207

Gnomad OTH exome AF: 0.214

GnomAD4 exome AF: 0.201 AC: 290554 AN: 1442882 Hom.: 30930 Cov.: 47 AF XY: 0.205 AC XY: 146779 AN XY: 717646

Gnomad4 AFR exome AF: 0.0295

Gnomad4 AMR exome AF: 0.109

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.236

Gnomad4 SAS exome AF: 0.274

Gnomad4 FIN exome AF: 0.231

Gnomad4 NFE exome AF: 0.202

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.153 AC: 23257 AN: 152182 Hom.: 2259 Cov.: 33 AF XY: 0.153 AC XY: 11406 AN XY: 74390

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.170

Alfa AF: 0.182 Hom.: 1398

Bravo AF: 0.142

Asia WGS AF: 0.232 AC: 805 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

ZNF804A-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	5.1
Dann	Benign	0.60

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: rs728534; hg19: chr2-185801917; COSMIC: COSV56436034;