2-184915494-C-G

Position:

• chr2-184915494-C-G

Variant summary

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

The NM_194250.2(ZNF804A):​c.256-18109C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,838 control chromosomes in the GnomAD database, including 24,690 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 0.56 (24690 hom., cov: 32)
• Consequence: ZNF804A NM_194250.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

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=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804A	NM_194250.2	c.256-18109C>G		intron_variant		ENST00000302277.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804A	ENST00000302277.7	c.256-18109C>G		intron_variant		1	NM_194250.2	P1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84674 AN: 151718 Hom.: 24681 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.558 AC: 84711 AN: 151838 Hom.: 24690 Cov.: 32 AF XY: 0.559 AC XY: 41442 AN XY: 74164

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.577

Alfa AF: 0.429 Hom.: 1192

Bravo AF: 0.565

Asia WGS AF: 0.649 AC: 2254 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.69

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: rs4666998; hg19: chr2-185780221;