rs6569792

Positions:

• chr6-132373612-A-G

Variant summary

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

The NM_015529.4(MOXD1):​c.412-615T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,980 control chromosomes in the GnomAD database, including 21,159 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 0.47 (21159 hom., cov: 31)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.412-615T>C		intron_variant		ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.307-615T>C		intron_variant			XP_016866203.1
MOXD1	XM_047418621.1	c.151-615T>C		intron_variant			XP_047274577.1
MOXD1	XM_047418622.1	c.151-615T>C		intron_variant			XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.412-615T>C		intron_variant		1	NM_015529.4	ENSP00000356940	P1
MOXD1	ENST00000336749.3	c.208-615T>C		intron_variant		1		ENSP00000336998

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71339 AN: 151862 Hom.: 21099 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.470 AC: 71461 AN: 151980 Hom.: 21159 Cov.: 31 AF XY: 0.470 AC XY: 34940 AN XY: 74286

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.452

Alfa AF: 0.333 Hom.: 12728

Bravo AF: 0.500

Asia WGS AF: 0.596 AC: 2070 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.43

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: rs6569792; hg19: chr6-132694751;