2-184642502-C-T

Position:

• chr2-184642502-C-T

Variant summary

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

The ENST00000302277.7(ZNF804A):​c.111+43432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,948 control chromosomes in the GnomAD database, including 25,108 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 (25108 hom., cov: 33)
• Consequence: ZNF804A ENST00000302277.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804A	NM_194250.2	c.111+43432C>T		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+43432C>T		intron_variant		1	NM_194250.2	ENSP00000303252	P1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85516 AN: 151830 Hom.: 25102 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.563 AC: 85558 AN: 151948 Hom.: 25108 Cov.: 33 AF XY: 0.555 AC XY: 41201 AN XY: 74298

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.552

Alfa AF: 0.534 Hom.: 4242

Bravo AF: 0.557

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.59

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: rs12693385; hg19: chr2-185507229;