rs6937164

chr6-132374173-A-Gchr6-132374173-A-T

Variant summary

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

The NM_015529.4(MOXD1):c.411+458T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,092 control chromosomes in the GnomAD database, including 20,443 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 0.44 (20443 hom., cov: 33)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

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 = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOXD1	NM_015529.4	c.411+458T>C		intron_variant		ENST00000367963.8
MOXD1	XM_017010714.3	c.306+458T>C		intron_variant
MOXD1	XM_047418621.1	c.150+458T>C		intron_variant
MOXD1	XM_047418622.1	c.150+458T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOXD1	ENST00000367963.8	c.411+458T>C		intron_variant		1	NM_015529.4	P1
MOXD1	ENST00000336749.3	c.207+458T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67280 AN: 151974 Hom.: 20380 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.443 AC: 67405 AN: 152092 Hom.: 20443 Cov.: 33 AF XY: 0.444 AC XY: 33002 AN XY: 74376

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.416

Alfa AF: 0.266 Hom.: 4144

Bravo AF: 0.472

Asia WGS AF: 0.566 AC: 1950 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.36

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: rs6937164; hg19: chr6-132695312;