ENST00000640078.1:n.475A>T

Variant names:

• chr2-184598458-T-A
• rs359895
• ENST00000640078.1:n.475A>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000640078.1(ENSG00000283839):​n.475A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,232 control chromosomes in the GnomAD database, including 24,556 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 (24515 hom., cov: 33)
  • Exomes 𝑓: 0.48 (41 hom.)
• Consequence: ENSG00000283839 ENST00000640078.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

Genes affected

ENSG00000283839 (HGNC:):

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373780	NR_171621.1	n.465A>T		non_coding_transcript_exon_variant	Exon 2 of 3
ZNF804A	NM_194250.2	c.-502T>A		upstream_gene_variant		ENST00000302277.7	NP_919226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804A	ENST00000302277.7	c.-502T>A		upstream_gene_variant		1	NM_194250.2	ENSP00000303252.6

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84319 AN: 150802 Hom.: 24512 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.481 AC: 155 AN: 322 Hom.: 41 Cov.: 0 AF XY: 0.486 AC XY: 108 AN XY: 222

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.0909

Gnomad4 SAS exome AF: 0.875

Gnomad4 FIN exome AF: 0.611

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.438

GnomAD4 genome AF: 0.559 AC: 84346 AN: 150910 Hom.: 24515 Cov.: 33 AF XY: 0.551 AC XY: 40613 AN XY: 73726

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.550

Alfa AF: 0.570 Hom.: 3151

Bravo AF: 0.553

Asia WGS AF: 0.323 AC: 1057 AN: 3274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	18
DANN	Benign	0.94

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: rs359895; hg19: chr2-185463185;