rs979606
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000240.4(MAOA):c.1165-55C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.72 ( 21061 hom., 23394 hem., cov: 23)
Exomes 𝑓: 0.68 ( 176704 hom. 240565 hem. )
Failed GnomAD Quality Control
Consequence
MAOA
NM_000240.4 intron
NM_000240.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.372
Genes affected
MAOA (HGNC:6833): (monoamine oxidase A) This gene is one of two neighboring gene family members that encode mitochondrial enzymes which catalyze the oxidative deamination of amines, such as dopamine, norepinephrine, and serotonin. Mutation of this gene results in Brunner syndrome. This gene has also been associated with a variety of other psychiatric disorders, including antisocial behavior. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAOA | NM_000240.4 | c.1165-55C>T | intron_variant | ENST00000338702.4 | NP_000231.1 | |||
MAOA | NM_001270458.2 | c.766-55C>T | intron_variant | NP_001257387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAOA | ENST00000338702.4 | c.1165-55C>T | intron_variant | 1 | NM_000240.4 | ENSP00000340684.3 |
Frequencies
GnomAD3 genomes AF: 0.723 AC: 80129AN: 110810Hom.: 21061 Cov.: 23 AF XY: 0.707 AC XY: 23347AN XY: 33016
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.684 AC: 746321AN: 1090492Hom.: 176704 AF XY: 0.673 AC XY: 240565AN XY: 357528
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.723 AC: 80172AN: 110867Hom.: 21061 Cov.: 23 AF XY: 0.707 AC XY: 23394AN XY: 33083
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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