Variant rs3918347 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001917.5(DAO):c.912+69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,331,902 control chromosomes in the GnomAD database, including 66,870 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9689 hom., cov: 32)

Exomes 𝑓: 0.30 ( 57181 hom. )

Consequence

DAO
NM_001917.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0350

Variant links:

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]

DAO links:

LOC124903011 (HGNC:):

LOC124903011 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 12-108899544-A-G is Benign according to our data. Variant chr12-108899544-A-G is described in ClinVar as [Benign]. Clinvar id is 1235637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAO	NM_001917.5 linkuse as main transcript	c.912+69A>G		intron_variant		ENST00000228476.8	NP_001908.3
LOC124903011	XR_007063453.1 linkuse as main transcript	n.519+434T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAO	ENST00000228476.8 linkuse as main transcript	c.912+69A>G		intron_variant		1	NM_001917.5	ENSP00000228476	P1

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52375

AN:

151902

Hom.:

9670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.380

GnomAD4 exome

AF:

0.300

AC:

354430

AN:

1179882

Hom.:

57181

Cov.:

AF XY:

0.302

AC XY:

179731

AN XY:

595262

show subpopulations

Gnomad4 AFR exome

AF:

0.408

Gnomad4 AMR exome

AF:

0.570

Gnomad4 ASJ exome

AF:

0.307

Gnomad4 EAS exome

AF:

0.469

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.294

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.345

AC:

52456

AN:

152020

Hom.:

9689

Cov.:

AF XY:

0.354

AC XY:

26270

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.309

Hom.:

4067

Bravo

AF:

0.365

Asia WGS

AF:

0.415

AC:

1442

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.81

DANN

Benign

0.78

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over