rs1935062

Positions:

• chr13-105475787-A-C
• chr13-105475787-A-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+3102A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,996 control chromosomes in the GnomAD database, including 8,735 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 0.33 (8735 hom., cov: 32)
• Consequence: DAOA NM_172370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAOA	NM_172370.5	c.281+3102A>C		intron_variant		ENST00000375936.9
DAOA-AS1	NR_040247.1	n.506-9367T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAOA	ENST00000375936.9	c.281+3102A>C		intron_variant		1	NM_172370.5	P2
DAOA-AS1	ENST00000448407.1	n.506-9367T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49873 AN: 151878 Hom.: 8732 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.328 AC: 49895 AN: 151996 Hom.: 8735 Cov.: 32 AF XY: 0.335 AC XY: 24913 AN XY: 74286

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.339

Alfa AF: 0.345 Hom.: 1896

Bravo AF: 0.321

Asia WGS AF: 0.445 AC: 1536 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.82

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: rs1935062; hg19: chr13-106128136;