rs7754123

Variant names:

• chr6-132346093-C-T
• rs7754123
• NM_015529.4:c.664-17499G>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.664-17499G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 151,520 control chromosomes in the GnomAD database, including 461 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 0.057 (461 hom., cov: 32)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.664-17499G>A		intron_variant	Intron 4 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.559-17499G>A		intron_variant	Intron 4 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.403-17499G>A		intron_variant	Intron 4 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.403-17499G>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.664-17499G>A		intron_variant	Intron 4 of 11	1	NM_015529.4	ENSP00000356940.3
MOXD1	ENST00000336749.3	c.460-17499G>A		intron_variant	Intron 3 of 10	1		ENSP00000336998.3

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 8616 AN: 151404 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.00579

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0161

Gnomad OTH AF: 0.0471

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

GnomAD4 genome AF: 0.0570 AC: 8639 AN: 151520 Hom.: 461 Cov.: 32 AF XY: 0.0581 AC XY: 4298 AN XY: 74022

African (AFR) AF: 0.139 AC: 5750 AN: 41248

American (AMR) AF: 0.0440 AC: 668 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.00579 AC: 20 AN: 3456

East Asian (EAS) AF: 0.0551 AC: 285 AN: 5168

South Asian (SAS) AF: 0.0610 AC: 292 AN: 4790

European-Finnish (FIN) AF: 0.0407 AC: 425 AN: 10454

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0161 AC: 1094 AN: 67912

Other (OTH) AF: 0.0471 AC: 99 AN: 2102

Alfa AF: 0.0510 Hom.: 75

Bravo AF: 0.0608

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.50
PhyloP100		0.024
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: rs7754123; hg19: chr6-132667232;