rs589756

Variant names:

• chr6-132321978-C-A
• rs589756
• NM_015529.4:c.1305+701G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-132321978-C-A
• chr6-132321978-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015529.4(MOXD1):​c.1305+701G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,088 control chromosomes in the GnomAD database, including 2,436 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 0.17 (2436 hom., cov: 32)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015529.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOXD1	NM_015529.4	MANE Select	c.1305+701G>T		intron	N/A	NP_056344.2	Q6UVY6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOXD1	ENST00000367963.8	TSL:1 MANE Select	c.1305+701G>T		intron	N/A	ENSP00000356940.3	Q6UVY6-1
	MOXD1	ENST00000336749.3	TSL:1	c.1101+701G>T		intron	N/A	ENSP00000336998.3	Q6UVY6-2
	MOXD1	ENST00000940886.1		c.1293+701G>T		intron	N/A	ENSP00000610945.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26596 AN: 151970 Hom.: 2437 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.157

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26592 AN: 152088 Hom.: 2436 Cov.: 32 AF XY: 0.168 AC XY: 12516 AN XY: 74370

African (AFR) AF: 0.166 AC: 6889 AN: 41466

American (AMR) AF: 0.149 AC: 2275 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.104 AC: 500 AN: 4824

European-Finnish (FIN) AF: 0.146 AC: 1540 AN: 10578

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14334 AN: 67978

Other (OTH) AF: 0.155 AC: 326 AN: 2110

Alfa AF: 0.196 Hom.: 8403

Bravo AF: 0.173

Asia WGS AF: 0.0500 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs589756;

hg19: chr6-132643117;

COSMIC: COSV60942867;