rs9301030

Positions:

• chr13-105473959-C-T

Variant summary

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

The NM_172370.5(DAOA):​c.281+1274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,852 control chromosomes in the GnomAD database, including 7,563 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 0.31 (7563 hom., cov: 31)
• Consequence: DAOA NM_172370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

Genes affected

DAOA (HGNC:21191): (D-amino acid oxidase activator) This gene encodes a protein that may function as an activator of D-amino acid oxidase, which degrades the gliotransmitter D-serine, a potent activator of N-methyl-D-aspartate (NMDA) type glutamate receptors. Studies also suggest that one encoded isoform may play a role in mitochondrial function and dendritic arborization. Polymorphisms in this gene have been implicated in susceptibility to schizophrenia and bipolar affective disorder. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Mar 2011]

DAOA-AS1 (HGNC:30243): (DAOA antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAOA	NM_172370.5	c.281+1274C>T		intron_variant		ENST00000375936.9	NP_758958.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAOA	ENST00000375936.9	c.281+1274C>T		intron_variant		1	NM_172370.5	ENSP00000365103.3
DAOA	ENST00000471432.3	n.*203-1018C>T		intron_variant		1		ENSP00000472857.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47438 AN: 151734 Hom.: 7552 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.313 AC: 47477 AN: 151852 Hom.: 7563 Cov.: 31 AF XY: 0.310 AC XY: 23013 AN XY: 74208

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.302

Alfa AF: 0.329 Hom.: 6074

Bravo AF: 0.310

Asia WGS AF: 0.255 AC: 888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.53

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: rs9301030; hg19: chr13-106126308;