rs1346551029

Variant names:

• chrX-43655100-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT-C
• rs1346551029
• NM_001270458.2:c.-1733_-1644delAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACC

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001270458.2(MAOA):​c.-1733_-1644delAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 3,061 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.00033 (0 hom. 0 hem.)
• Consequence: MAOA NM_001270458.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 0 publications found

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]

MAOA Gene-Disease associations (from GenCC):

• Brunner syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_001270458.2	c.-1733_-1644delAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACC		5_prime_UTR_variant	Exon 1 of 16		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000542639.6	c.-1733_-1644delAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACC		5_prime_UTR_variant	Exon 1 of 16	2		ENSP00000440846.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 0.000327 AC: 1 AN: 3061 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1329

African (AFR) AF: 0.00 AC: 0 AN: 65

American (AMR) AF: 0.00 AC: 0 AN: 64

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 39

East Asian (EAS) AF: 0.00 AC: 0 AN: 71

South Asian (SAS) AF: 0.00 AC: 0 AN: 380

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 93

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.000448 AC: 1 AN: 2231

Other (OTH) AF: 0.00 AC: 0 AN: 112

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs1346551029; hg19: chrX-43514348;