rs12613195

Positions:

• chr2-184624494-C-G

Variant summary

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

The ENST00000302277.7(ZNF804A):​c.111+25424C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,068 control chromosomes in the GnomAD database, including 6,217 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 0.26 (6217 hom., cov: 32)
• Consequence: ZNF804A ENST00000302277.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804A	NM_194250.2	c.111+25424C>G		intron_variant		ENST00000302277.7	NP_919226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804A	ENST00000302277.7	c.111+25424C>G		intron_variant		1	NM_194250.2	ENSP00000303252	P1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39382 AN: 151952 Hom.: 6221 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.259 AC: 39383 AN: 152068 Hom.: 6217 Cov.: 32 AF XY: 0.265 AC XY: 19659 AN XY: 74318

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.255

Alfa AF: 0.273 Hom.: 801

Bravo AF: 0.249

Asia WGS AF: 0.363 AC: 1260 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.28

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: rs12613195; hg19: chr2-185489221;