rs3931790

chr2-184898649-A-C

Variant summary

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

The NM_194250.2(ZNF804A):c.255+32137A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,040 control chromosomes in the GnomAD database, including 2,248 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 0.15 (2248 hom., cov: 32)
• Consequence: ZNF804A NM_194250.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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 -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 = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804A	NM_194250.2	c.255+32137A>C		intron_variant		ENST00000302277.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804A	ENST00000302277.7	c.255+32137A>C		intron_variant		1	NM_194250.2	P1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22995 AN: 151922 Hom.: 2250 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.146

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152040 Hom.: 2248 Cov.: 32 AF XY: 0.152 AC XY: 11291 AN XY: 74310

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.144

Alfa AF: 0.161 Hom.: 285

Bravo AF: 0.151

Asia WGS AF: 0.192 AC: 666 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.0
Dann	Benign	0.77

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: rs3931790; hg19: chr2-185763376;