13-105478789-C-T

Position:

• chr13-105478789-C-T

Variant summary

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

The ENST00000375936.9(DAOA):​c.281+6104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,958 control chromosomes in the GnomAD database, including 25,115 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 0.57 (25115 hom., cov: 33)
• Consequence: DAOA ENST00000375936.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAOA	NM_172370.5	c.281+6104C>T		intron_variant		ENST00000375936.9	NP_758958.3
DAOA-AS1	NR_040247.1	n.505+10987G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAOA	ENST00000375936.9	c.281+6104C>T		intron_variant		1	NM_172370.5	ENSP00000365103	P2
DAOA-AS1	ENST00000448407.1	n.505+10987G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86740 AN: 151842 Hom.: 25100 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.571 AC: 86798 AN: 151958 Hom.: 25115 Cov.: 33 AF XY: 0.577 AC XY: 42870 AN XY: 74302

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.593

Alfa AF: 0.526 Hom.: 7688

Bravo AF: 0.569

Asia WGS AF: 0.754 AC: 2621 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	0.49
DANN	Benign	0.39

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: rs2153674; hg19: chr13-106131138;