rs2111902

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -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

Publications

25 publications found

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 Gene-Disease associations (from GenCC):

amyotrophic lateral sclerosis
Inheritance: AD Classification: MODERATE, SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Genomics England PanelApp, ClinGen, Orphanet

DAO links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001917.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001917.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DAO	NM_001917.5	MANE Select	c.-9-27T>G	intron	N/A	NP_001908.3
DAO	NM_001413634.1		c.-9-27T>G	intron	N/A	NP_001400563.1	P14920
DAO	NM_001413635.1		c.-9-27T>G	intron	N/A	NP_001400564.1	A0A0S2Z3J4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DAO	ENST00000228476.8	TSL:1 MANE Select	c.-9-27T>G	intron	N/A	ENSP00000228476.3	P14920
DAO	ENST00000551281.5	TSL:1	c.-9-27T>G	intron	N/A	ENSP00000446853.1	A0A0B4J250
DAO	ENST00000547122.5	TSL:1	n.-9-27T>G	intron	N/A	ENSP00000448095.1	A0A0B4J257

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

GnomAD2 exomes

AF:

0.398

AC:

99716

AN:

250800

AF XY:

0.390

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 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

African (AFR)

AF:

0.561

AC:

18655

AN:

33280

American (AMR)

AF:

0.595

AC:

26584

AN:

44702

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

9681

AN:

26082

East Asian (EAS)

AF:

0.478

AC:

18952

AN:

39634

South Asian (SAS)

AF:

0.469

AC:

40392

AN:

86068

European-Finnish (FIN)

AF:

0.316

AC:

16818

AN:

53268

Middle Eastern (MID)

AF:

0.461

AC:

2652

AN:

5756

European-Non Finnish (NFE)

AF:

0.294

AC:

323819

AN:

1103084

Other (OTH)

AF:

0.357

AC:

21430

AN:

60016

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

16596

33191

49787

66382

82978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11116

22232

33348

44464

55580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.404

AC:

61310

AN:

151934

Hom.:

13550

Cov.:

AF XY:

0.411

AC XY:

30537

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.548

AC:

22684

AN:

41394

American (AMR)

AF:

0.534

AC:

8150

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

1291

AN:

3468

East Asian (EAS)

AF:

0.491

AC:

2537

AN:

5170

South Asian (SAS)

AF:

0.470

AC:

2264

AN:

4816

European-Finnish (FIN)

AF:

0.333

AC:

3513

AN:

10562

Middle Eastern (MID)

AF:

0.452

AC:

133

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19565

AN:

67964

Other (OTH)

AF:

0.432

AC:

911

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1744

3488

5232

6976

8720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

566

1132

1698

2264

2830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.320

Hom.:

22090

Bravo

AF:

0.427

Asia WGS

AF:

0.449

AC:

1563

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.4

(source)

DANN

Benign

0.62

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over