rs6323
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The ENST00000338702.4(MAOA):c.891G>T(p.Arg297=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.72 ( 21051 hom., 22800 hem., cov: 23)
Exomes 𝑓: 0.68 ( 177110 hom. 243137 hem. )
Failed GnomAD Quality Control
Consequence
MAOA
ENST00000338702.4 synonymous
ENST00000338702.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.300
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 Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant X-43731789-G-T is Benign according to our data. Variant chrX-43731789-G-T is described in ClinVar as [Benign]. Clinvar id is 92664.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-43731789-G-T is described in Lovd as [Benign]. Variant chrX-43731789-G-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.3 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAOA | NM_000240.4 | c.891G>T | p.Arg297= | synonymous_variant | 8/15 | ENST00000338702.4 | NP_000231.1 | |
MAOA | NM_001270458.2 | c.492G>T | p.Arg164= | synonymous_variant | 9/16 | NP_001257387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAOA | ENST00000338702.4 | c.891G>T | p.Arg297= | synonymous_variant | 8/15 | 1 | NM_000240.4 | ENSP00000340684 | P1 |
Frequencies
GnomAD3 genomes AF: 0.722 AC: 79528AN: 110183Hom.: 21051 Cov.: 23 AF XY: 0.703 AC XY: 22754AN XY: 32385
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GnomAD3 exomes AF: 0.650 AC: 118872AN: 182873Hom.: 26030 AF XY: 0.634 AC XY: 42749AN XY: 67445
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.684 AC: 749816AN: 1096495Hom.: 177110 Cov.: 34 AF XY: 0.671 AC XY: 243137AN XY: 362185
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.722 AC: 79570AN: 110234Hom.: 21051 Cov.: 23 AF XY: 0.703 AC XY: 22800AN XY: 32446
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 16, 2015 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Brunner syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2015 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational 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