rs2275394

Positions:

• chr6-132390061-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.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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.264+11102A>G		intron_variant		ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.159+11207A>G		intron_variant			XP_016866203.1
MOXD1	XM_047418622.1	c.3+1646A>G		intron_variant			XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.264+11102A>G		intron_variant		1	NM_015529.4	ENSP00000356940	P1

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

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.398

Alfa AF: 0.271 Hom.: 6382

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

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: rs2275394; hg19: chr6-132711200; COSMIC: COSV63452482; COSMIC: COSV63452482;