rs2070586

chr12-108883944-G-A

Variant summary

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

The NM_001917.5(DAO):c.-9-1054G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,226 control chromosomes in the GnomAD database, including 6,093 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 0.26 (6093 hom., cov: 33)
• Consequence: DAO NM_001917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970

Genes affected

DAO (HGNC:2671): (D-amino acid oxidase) This gene encodes the peroxisomal enzyme D-amino acid oxidase. The enzyme is a flavoprotein which uses flavin adenine dinucleotide (FAD) as its prosthetic group. Its substrates include a wide variety of D-amino acids, but it is inactive on the naturally occurring L-amino acids. Its biological function is not known; it may act as a detoxifying agent which removes D-amino acids that accumulate during aging. In mice, it degrades D-serine, a co-agonist of the NMDA receptor. This gene may play a role in the pathophysiology of schizophrenia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAO	NM_001917.5	c.-9-1054G>A		intron_variant		ENST00000228476.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAO	ENST00000228476.8	c.-9-1054G>A		intron_variant		1	NM_001917.5	P1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39092 AN: 152108 Hom.: 6073 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.257 AC: 39165 AN: 152226 Hom.: 6093 Cov.: 33 AF XY: 0.262 AC XY: 19528 AN XY: 74422

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.253

Alfa AF: 0.184 Hom.: 5992

Bravo AF: 0.277

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.7
Dann	Benign	0.69

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: rs2070586; hg19: chr12-109277720;