rs369122751
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000240.4(MAOA):c.412-6C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,181,125 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 63 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000240.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAOA | NM_000240.4 | c.412-6C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000338702.4 | |||
MAOA | NM_001270458.2 | c.13-6C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAOA | ENST00000338702.4 | c.412-6C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000240.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000108 AC: 12AN: 111079Hom.: 0 Cov.: 23 AF XY: 0.0000601 AC XY: 2AN XY: 33277
GnomAD3 exomes AF: 0.0000662 AC: 12AN: 181299Hom.: 0 AF XY: 0.0000908 AC XY: 6AN XY: 66073
GnomAD4 exome AF: 0.000207 AC: 222AN: 1069996Hom.: 0 Cov.: 26 AF XY: 0.000180 AC XY: 61AN XY: 339526
GnomAD4 genome ? AF: 0.000108 AC: 12AN: 111129Hom.: 0 Cov.: 23 AF XY: 0.0000600 AC XY: 2AN XY: 33337
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 22, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2022 | This alteration is classified as likely 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. - |
Brunner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at