Variant 12-108884971-T-G 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.-9-27T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,603,824 control chromosomes in the GnomAD database, including 98,144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 13550 hom., cov: 32)

Exomes 𝑓: 0.33 ( 84594 hom. )

Consequence

DAO
NM_001917.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.557

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:

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 12-108884971-T-G is Benign according to our data. Variant chr12-108884971-T-G is described in ClinVar as [Benign]. Clinvar id is 1243869.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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.-9-27T>G		intron_variant		ENST00000228476.8	NP_001908.3	P14920A0A024RBI1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAO	ENST00000228476.8 linkuse as main transcript	c.-9-27T>G		intron_variant		1	NM_001917.5	ENSP00000228476.3		P14920

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61210

AN:

151816

Hom.:

13516

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.429

GnomAD3 exomes

AF:

0.398

AC:

99716

AN:

250800

Hom.:

21899

AF XY:

0.390

AC XY:

52887

AN XY:

135618

show subpopulations

Gnomad AFR exome

AF:

0.546

Gnomad AMR exome

AF:

0.603

Gnomad ASJ exome

AF:

0.376

Gnomad EAS exome

AF:

0.501

Gnomad SAS exome

AF:

0.465

Gnomad FIN exome

AF:

0.326

Gnomad NFE exome

AF:

0.295

Gnomad OTH exome

AF:

0.375

GnomAD4 exome

AF:

0.330

AC:

478983

AN:

1451890

Hom.:

84594

Cov.:

AF XY:

0.333

AC XY:

240568

AN XY:

723068

show subpopulations

Gnomad4 AFR exome

AF:

0.561

Gnomad4 AMR exome

AF:

0.595

Gnomad4 ASJ exome

AF:

0.371

Gnomad4 EAS exome

AF:

0.478

Gnomad4 SAS exome

AF:

0.469

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.357

GnomAD4 genome

AF:

0.404

AC:

61310

AN:

151934

Hom.:

13550

Cov.:

AF XY:

0.411

AC XY:

30537

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.548

Gnomad4 AMR

AF:

0.534

Gnomad4 ASJ

AF:

0.372

Gnomad4 EAS

AF:

0.491

Gnomad4 SAS

AF:

0.470

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.432

Alfa

AF:

0.315

Hom.:

16881

Bravo

AF:

0.427

Asia WGS

AF:

0.449

AC:

1563

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

2.4

DANN

Benign

0.62

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