Variant rs3046266 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PM4_SupportingBA1

The NM_194250.2(ZNF804A):c.2090_2092dupCAA(p.Thr697dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,603,270 control chromosomes in the GnomAD database, including 273,085 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 20581 hom., cov: 0)

Exomes 𝑓: 0.58 ( 252504 hom. )

Consequence

ZNF804A
NM_194250.2 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76

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 -7 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_194250.2. Strenght limited to Supporting due to length of the change: 1aa.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804A	NM_194250.2 link	c.2090_2092dupCAA	p.Thr697dup	disruptive_inframe_insertion	4/4	ENST00000302277.7	NP_919226.1	Q7Z570

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804A	ENST00000302277.7 link	c.2090_2092dupCAA	p.Thr697dup	disruptive_inframe_insertion	4/4	1	NM_194250.2	ENSP00000303252.6		Q7Z570

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71786

AN:

151652

Hom.:

20582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.644

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.832

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.627

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.579

Gnomad OTH

AF:

0.500

GnomAD3 exomes

AF:

0.592

AC:

143790

AN:

242768

Hom.:

45868

AF XY:

0.591

AC XY:

77704

AN XY:

131578

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.716

Gnomad ASJ exome

AF:

0.614

Gnomad EAS exome

AF:

0.847

Gnomad SAS exome

AF:

0.541

Gnomad FIN exome

AF:

0.645

Gnomad NFE exome

AF:

0.582

Gnomad OTH exome

AF:

0.591

GnomAD4 exome

AF:

0.581

AC:

843742

AN:

1451498

Hom.:

252504

Cov.:

AF XY:

0.581

AC XY:

419326

AN XY:

722000

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.707

Gnomad4 ASJ exome

AF:

0.609

Gnomad4 EAS exome

AF:

0.844

Gnomad4 SAS exome

AF:

0.547

Gnomad4 FIN exome

AF:

0.640

Gnomad4 NFE exome

AF:

0.582

Gnomad4 OTH exome

AF:

0.560

GnomAD4 genome

AF:

0.473

AC:

71787

AN:

151772

Hom.:

20581

Cov.:

AF XY:

0.479

AC XY:

35532

AN XY:

74172

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.644

Gnomad4 ASJ

AF:

0.607

Gnomad4 EAS

AF:

0.832

Gnomad4 SAS

AF:

0.542

Gnomad4 FIN

AF:

0.627

Gnomad4 NFE

AF:

0.579

Gnomad4 OTH

AF:

0.496

Alfa

AF:

0.527

Hom.:

3823

Asia WGS

AF:

0.616

AC:

2139

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over