rs2275394

Variant names:

• chr6-132390061-T-C
• rs2275394
• NM_015529.4:c.264+11102A>G

Variant summary

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

The NM_015529.4(MOXD1):​c.264+11102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,078 control chromosomes in the GnomAD database, including 19,312 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 0.42 (19312 hom., cov: 32)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.264+11102A>G		intron_variant	Intron 1 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.159+11207A>G		intron_variant	Intron 1 of 11		XP_016866203.1
MOXD1	XM_047418622.1	c.3+1646A>G		intron_variant	Intron 1 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.264+11102A>G		intron_variant	Intron 1 of 11	1	NM_015529.4	ENSP00000356940.3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 63937 AN: 150962 Hom.: 19254 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.0982

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.387

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.424 AC: 64055 AN: 151078 Hom.: 19312 Cov.: 32 AF XY: 0.425 AC XY: 31344 AN XY: 73786

African (AFR) AF: 0.809 AC: 33488 AN: 41408

American (AMR) AF: 0.369 AC: 5558 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1070 AN: 3450

East Asian (EAS) AF: 0.650 AC: 3353 AN: 5158

South Asian (SAS) AF: 0.349 AC: 1643 AN: 4706

European-Finnish (FIN) AF: 0.232 AC: 2438 AN: 10524

Middle Eastern (MID) AF: 0.378 AC: 109 AN: 288

European-Non Finnish (NFE) AF: 0.229 AC: 15482 AN: 67518

Other (OTH) AF: 0.398 AC: 828 AN: 2080

Alfa AF: 0.280 Hom.: 8043

Bravo AF: 0.451

Asia WGS AF: 0.532 AC: 1844 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		-0.44
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: rs2275394; hg19: chr6-132711200; COSMIC: COSV63452482; COSMIC: COSV63452482;