13-105465643-A-G

Variant names:

• chr13-105465643-A-G
• rs1361562
• ENST00000448407.1:n.739+544T>C

Variant summary

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

The ENST00000448407.1(DAOA-AS1):​n.739+544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,286 control chromosomes in the GnomAD database, including 71,140 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 0.97 (71140 hom., cov: 33)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 2 publications found

Genes affected

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

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAOA-AS1	NR_040247.1	n.739+544T>C		intron_variant	Intron 5 of 6
DAOA	NM_001161814.1	c.-750A>G		upstream_gene_variant			NP_001155286.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.739+544T>C		intron_variant	Intron 5 of 6	2
DAOA	ENST00000559369.5	n.-750A>G		upstream_gene_variant		1		ENSP00000453831.1

Frequencies

GnomAD3 genomes AF: 0.966 AC: 146935 AN: 152168 Hom.: 71102 Cov.: 33

Gnomad AFR AF: 0.890

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.979

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.965 AC: 147025 AN: 152286 Hom.: 71140 Cov.: 33 AF XY: 0.966 AC XY: 71900 AN XY: 74444

African (AFR) AF: 0.889 AC: 36952 AN: 41546

American (AMR) AF: 0.985 AC: 15063 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3430 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5168 AN: 5168

South Asian (SAS) AF: 0.979 AC: 4727 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10624 AN: 10626

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67801 AN: 68034

Other (OTH) AF: 0.977 AC: 2065 AN: 2114

Alfa AF: 0.966 Hom.: 10031

Bravo AF: 0.961

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.57
PhyloP100		-0.18
PromoterAI		-0.0068	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1361562; hg19: chr13-106117992;