rs1981187

Variant names:

• chr6-132359427-C-T
• rs1981187
• NM_015529.4:c.663+13181G>A

Variant summary

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

The NM_015529.4(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 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608
• Publications: 0 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=-0.63).
• 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 rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.663+13181G>A		intron_variant	Intron 4 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.558+13181G>A		intron_variant	Intron 4 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.402+13181G>A		intron_variant	Intron 4 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.402+13181G>A		intron_variant	Intron 4 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.663+13181G>A		intron_variant	Intron 4 of 11	1	NM_015529.4	ENSP00000356940.3
MOXD1	ENST00000336749.3	c.459+13181G>A		intron_variant	Intron 3 of 10	1		ENSP00000336998.3

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

African (AFR) AF: 0.838 AC: 34541 AN: 41214

American (AMR) AF: 0.386 AC: 5881 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3707 AN: 5130

South Asian (SAS) AF: 0.386 AC: 1847 AN: 4790

European-Finnish (FIN) AF: 0.182 AC: 1852 AN: 10200

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14458 AN: 67870

Other (OTH) AF: 0.395 AC: 830 AN: 2100

Alfa AF: 0.345 Hom.: 3812

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
PhyloP100		0.61
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

Other links and lift over

dbSNP: rs1981187; hg19: chr6-132680566;