13-105468636-G-T

Position:

• chr13-105468636-G-T

Variant summary

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

The NM_172370.5(DAOA):​c.133+1495G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,206 control chromosomes in the GnomAD database, including 1,141 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 0.12 (1141 hom., cov: 33)
• Consequence: DAOA NM_172370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAOA	NM_172370.5	c.133+1495G>T		intron_variant		ENST00000375936.9	NP_758958.3
DAOA-AS1	NR_040247.1	n.506-2216C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAOA	ENST00000375936.9	c.133+1495G>T		intron_variant		1	NM_172370.5	ENSP00000365103	P2
DAOA-AS1	ENST00000448407.1	n.506-2216C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17779 AN: 152088 Hom.: 1141 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.117 AC: 17781 AN: 152206 Hom.: 1141 Cov.: 33 AF XY: 0.113 AC XY: 8382 AN XY: 74394

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0662

Gnomad4 FIN AF: 0.0833

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0945 Hom.: 274

Bravo AF: 0.121

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.58

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: rs12874006; hg19: chr13-106120985;