Variant 2-184937190-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

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 (no stars).

Frequency

Genomes: 𝑓 0.15 ( 2259 hom., cov: 33)

Exomes 𝑓: 0.20 ( 30930 hom. )

Consequence

ZNF804A
NM_194250.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.00

Variant links:

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]

ZNF804A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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 no_assertion_criteria_provided, 0 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 linkuse as main transcript	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 linkuse as main transcript	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.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.205

AC XY:

146779

AN XY:

717646

show subpopulations

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.:

AF XY:

0.153

AC XY:

11406

AN XY:

74390

show subpopulations

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: no assertion criteria provided

LINK: link

Submissions by phenotype

ZNF804A-related disorder

Benign:1

Benign, no assertion criteria provided

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over