rs13393273

Variant names:

• chr2-184612950-A-G
• rs13393273
• NM_194250.2:c.111+13880A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194250.2(ZNF804A):​c.111+13880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,068 control chromosomes in the GnomAD database, including 12,468 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 0.40 (12468 hom., cov: 33)
• Consequence: ZNF804A NM_194250.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804A	NM_194250.2	c.111+13880A>G		intron_variant	Intron 1 of 3	ENST00000302277.7	NP_919226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804A	ENST00000302277.7	c.111+13880A>G		intron_variant	Intron 1 of 3	1	NM_194250.2	ENSP00000303252.6

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60660 AN: 151950 Hom.: 12455 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.399 AC: 60707 AN: 152068 Hom.: 12468 Cov.: 33 AF XY: 0.396 AC XY: 29443 AN XY: 74342

African (AFR) AF: 0.455 AC: 18847 AN: 41458

American (AMR) AF: 0.296 AC: 4520 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.163 AC: 845 AN: 5182

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4165 AN: 10566

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27604 AN: 67958

Other (OTH) AF: 0.399 AC: 842 AN: 2112

Alfa AF: 0.418 Hom.: 1776

Bravo AF: 0.391

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.99
DANN	Benign	0.62
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13393273; hg19: chr2-185477677;