Variant 13-105489886-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001161812.1(DAOA):c.183C>T(p.Thr61Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,613,382 control chromosomes in the GnomAD database, including 65,280 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 ( 5265 hom., cov: 31)

Exomes 𝑓: 0.28 ( 60015 hom. )

Consequence

DAOA
NM_001161812.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Variant links:

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 links:

DAOA-AS1 (HGNC:):

DAOA-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP7

Synonymous conserved (PhyloP=-2.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAOA	NM_172370.5 linkuse as main transcript	c.282-15C>T		intron_variant		ENST00000375936.9	NP_758958.3	P59103-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DAOA	ENST00000375936.9 linkuse as main transcript	c.282-15C>T	intron_variant		1	NM_172370.5	ENSP00000365103.3	P59103-1
DAOA	ENST00000471432.3 linkuse as main transcript	n.*487C>T	non_coding_transcript_exon_variant	6/7	1		ENSP00000472857.1	M0R2W9
DAOA	ENST00000471432.3 linkuse as main transcript	n.*487C>T	3_prime_UTR_variant	6/7	1		ENSP00000472857.1	M0R2W9

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39396

AN:

151742

Hom.:

5259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.290

Gnomad OTH

AF:

0.249

GnomAD3 exomes

AF:

0.266

AC:

65632

AN:

246952

Hom.:

9191

AF XY:

0.261

AC XY:

35000

AN XY:

134062

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.262

Gnomad EAS exome

AF:

0.134

Gnomad SAS exome

AF:

0.203

Gnomad FIN exome

AF:

0.291

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.283

AC:

413162

AN:

1461522

Hom.:

60015

Cov.:

AF XY:

0.280

AC XY:

203438

AN XY:

727052

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.296

Gnomad4 OTH exome

AF:

0.264

GnomAD4 genome

AF:

0.260

AC:

39419

AN:

151860

Hom.:

5265

Cov.:

AF XY:

0.257

AC XY:

19076

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.290

Gnomad4 OTH

AF:

0.248

Alfa

AF:

0.280

Hom.:

14183

Bravo

AF:

0.259

Asia WGS

AF:

0.177

AC:

619

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.27

DANN

Benign

0.51

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over