rs1981187

Positions:

• chr6-132359427-C-T

Variant summary

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

The ENST00000367963.8(MOXD1):​c.663+13181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,202 control chromosomes in the GnomAD database, including 19,549 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 0.43 (19549 hom., cov: 31)
• Consequence: MOXD1 ENST00000367963.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.663+13181G>A		intron_variant		ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.558+13181G>A		intron_variant			XP_016866203.1
MOXD1	XM_047418621.1	c.402+13181G>A		intron_variant			XP_047274577.1
MOXD1	XM_047418622.1	c.402+13181G>A		intron_variant			XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.663+13181G>A		intron_variant		1	NM_015529.4	ENSP00000356940	P1
MOXD1	ENST00000336749.3	c.459+13181G>A		intron_variant		1		ENSP00000336998

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64164 AN: 151094 Hom.: 19492 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.425 AC: 64283 AN: 151202 Hom.: 19549 Cov.: 31 AF XY: 0.425 AC XY: 31402 AN XY: 73826

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.395

Alfa AF: 0.325 Hom.: 1526

Bravo AF: 0.459

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	5.7
DANN	Benign	0.51

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: rs1981187; hg19: chr6-132680566;