rs9388989

Positions:

• chr6-132376443-G-A
• chr6-132376443-G-T

Variant summary

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

The NM_015529.4(MOXD1):​c.265-1666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 145,846 control chromosomes in the GnomAD database, including 19,842 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 0.44 (19842 hom., cov: 30)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOXD1	NM_015529.4	c.265-1666C>T		intron_variant		ENST00000367963.8
MOXD1	XM_017010714.3	c.160-1666C>T		intron_variant
MOXD1	XM_047418621.1	c.4-1666C>T		intron_variant
MOXD1	XM_047418622.1	c.4-1666C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOXD1	ENST00000367963.8	c.265-1666C>T		intron_variant		1	NM_015529.4	P1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 64648 AN: 145742 Hom.: 19782 Cov.: 30

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.444 AC: 64770 AN: 145846 Hom.: 19842 Cov.: 30 AF XY: 0.449 AC XY: 31710 AN XY: 70588

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.411

Alfa AF: 0.269 Hom.: 9701

Bravo AF: 0.460

Asia WGS AF: 0.563 AC: 1955 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.63

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: rs9388989; hg19: chr6-132697582;