6-132366903-T-C

Position:

• chr6-132366903-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.663+5705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,858 control chromosomes in the GnomAD database, including 12,645 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 0.36 (12645 hom., cov: 32)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOXD1	NM_015529.4	c.663+5705A>G		intron_variant		ENST00000367963.8
MOXD1	XM_017010714.3	c.558+5705A>G		intron_variant
MOXD1	XM_047418621.1	c.402+5705A>G		intron_variant
MOXD1	XM_047418622.1	c.402+5705A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOXD1	ENST00000367963.8	c.663+5705A>G		intron_variant		1	NM_015529.4	P1
MOXD1	ENST00000336749.3	c.459+5705A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54600 AN: 151740 Hom.: 12608 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.360 AC: 54690 AN: 151858 Hom.: 12645 Cov.: 32 AF XY: 0.362 AC XY: 26895 AN XY: 74232

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.342

Alfa AF: 0.255 Hom.: 1215

Bravo AF: 0.385

Asia WGS AF: 0.550 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.084
DANN	Benign	0.40

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: rs1338387; hg19: chr6-132688042;