rs2206064

chr6-132299855-T-C

Variant summary

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

The NM_015529.4(MOXD1):c.1509-1900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 151,954 control chromosomes in the GnomAD database, including 609 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 0.056 (609 hom., cov: 31)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOXD1	NM_015529.4	c.1509-1900A>G		intron_variant		ENST00000367963.8
MOXD1	XM_017010714.3	c.1404-1900A>G		intron_variant
MOXD1	XM_047418621.1	c.1248-1900A>G		intron_variant
MOXD1	XM_047418622.1	c.1248-1900A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOXD1	ENST00000367963.8	c.1509-1900A>G		intron_variant		1	NM_015529.4	P1
MOXD1	ENST00000336749.3	c.1305-1900A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8456 AN: 151838 Hom.: 608 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.00917

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00706

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0558 AC: 8480 AN: 151954 Hom.: 609 Cov.: 31 AF XY: 0.0570 AC XY: 4235 AN XY: 74268

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.00917

Gnomad4 NFE AF: 0.00705

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0330 Hom.: 27

Bravo AF: 0.0676

Asia WGS AF: 0.145 AC: 500 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.48
Dann	Benign	0.49

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: rs2206064; hg19: chr6-132620994;