rs3734744

Positions:

• chr6-132374877-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336749.3(MOXD1):​c.-40A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,214,052 control chromosomes in the GnomAD database, including 30,572 homozygotes. 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 0.30 (10539 hom., cov: 33)
  • Exomes 𝑓: 0.17 (20033 hom.)
• Consequence: MOXD1 ENST00000336749.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42

Genes affected

MOXD1 (HGNC:21063): (monooxygenase DBH like 1) Predicted to enable copper ion binding activity and dopamine beta-monooxygenase activity. Predicted to be involved in dopamine catabolic process; norepinephrine biosynthetic process; and octopamine biosynthetic process. Part of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.265-100A>C		intron_variant		ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.160-100A>C		intron_variant			XP_016866203.1
MOXD1	XM_047418621.1	c.4-100A>C		intron_variant			XP_047274577.1
MOXD1	XM_047418622.1	c.4-100A>C		intron_variant			XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000336749.3	c.-40A>C		5_prime_UTR_variant	1/11	1		ENSP00000336998.3
MOXD1	ENST00000367963.8	c.265-100A>C		intron_variant		1	NM_015529.4	ENSP00000356940.3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45896 AN: 152014 Hom.: 10513 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.277

GnomAD3 exomes AF: 0.214 AC: 27396 AN: 127806 Hom.: 3930 AF XY: 0.209 AC XY: 14051 AN XY: 67122

Gnomad AFR exome AF: 0.669

Gnomad AMR exome AF: 0.155

Gnomad ASJ exome AF: 0.172

Gnomad EAS exome AF: 0.261

Gnomad SAS exome AF: 0.264

Gnomad FIN exome AF: 0.142

Gnomad NFE exome AF: 0.166

Gnomad OTH exome AF: 0.190

GnomAD4 exome AF: 0.173 AC: 183926 AN: 1061920 Hom.: 20033 Cov.: 14 AF XY: 0.174 AC XY: 93171 AN XY: 535584

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.158

Gnomad4 ASJ exome AF: 0.157

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.246

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.204

GnomAD4 genome AF: 0.302 AC: 45983 AN: 152132 Hom.: 10539 Cov.: 33 AF XY: 0.298 AC XY: 22152 AN XY: 74394

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.282

Alfa AF: 0.184 Hom.: 4606

Bravo AF: 0.322

Asia WGS AF: 0.318 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.3
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734744; hg19: chr6-132696016;