rs1346551029

Positions:

• chrX-43655100-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT-C
• chrX-43655100-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT-CACCGGCACCGGCACCAGTACCCGCACCAGT
• chrX-43655100-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001270458.2(MAOA):​c.-1703_-1644del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000645 in 62,002 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000065 (0 hom., 0 hem., cov: 24)
  • Exomes 𝑓: 0.00033 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_001270458.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOA	NM_001270458.2	c.-1703_-1644del		5_prime_UTR_variant	1/16		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000542639.6	c.-1703_-1644del		5_prime_UTR_variant	1/16	2		ENSP00000440846

Frequencies

GnomAD3 genomes AF: 0.0000645 AC: 4 AN: 62002 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 19076

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000436

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000369

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000327 AC: 1 AN: 3061 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1329

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000448

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000645 AC: 4 AN: 62002 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 19076

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000373

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000436

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000369

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1346551029; hg19: chrX-43514348;