13-105490025-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_172370.5(DAOA):c.406C>G(p.Gln136Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000682 in 1,608,548 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00037 ( 7 hom. )
Consequence
DAOA
NM_172370.5 missense
NM_172370.5 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: -0.699
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004847318).
BP6
?
Variant 13-105490025-C-G is Benign according to our data. Variant chr13-105490025-C-G is described in ClinVar as [Benign]. Clinvar id is 768629.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAOA | NM_172370.5 | c.406C>G | p.Gln136Glu | missense_variant | 5/6 | ENST00000375936.9 | |
DAOA-AS1 | NR_040247.1 | n.264-8G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAOA | ENST00000375936.9 | c.406C>G | p.Gln136Glu | missense_variant | 5/6 | 1 | NM_172370.5 | P2 | |
DAOA-AS1 | ENST00000448407.1 | n.264-8G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00372 AC: 565AN: 152034Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000984 AC: 229AN: 232748Hom.: 4 AF XY: 0.000805 AC XY: 102AN XY: 126648
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GnomAD4 exome AF: 0.000365 AC: 532AN: 1456396Hom.: 7 Cov.: 32 AF XY: 0.000327 AC XY: 237AN XY: 724078
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GnomAD4 genome ? AF: 0.00371 AC: 565AN: 152152Hom.: 3 Cov.: 32 AF XY: 0.00332 AC XY: 247AN XY: 74390
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;.;.
REVEL
Benign
Sift
Pathogenic
D;D;.;.
Sift4G
Pathogenic
D;D;D;D
Polyphen
B;.;B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at