rs15017

Positions:

• chr6-132296235-C-G

Variant summary

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

The NM_015529.4(MOXD1):​c.*918G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,058 control chromosomes in the GnomAD database, including 355 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 0.060 (355 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MOXD1 NM_015529.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

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 (SAS) allele frequency at 95% confidence interval = 0.0995 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.*918G>C		3_prime_UTR_variant	12/12	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.*918G>C		3_prime_UTR_variant	12/12		XP_016866203.1
MOXD1	XM_047418621.1	c.*918G>C		3_prime_UTR_variant	12/12		XP_047274577.1
MOXD1	XM_047418622.1	c.*918G>C		3_prime_UTR_variant	12/12		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.*918G>C		3_prime_UTR_variant	12/12	1	NM_015529.4	ENSP00000356940	P1
MOXD1	ENST00000336749.3	c.*918G>C		3_prime_UTR_variant	11/11	1		ENSP00000336998

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9181 AN: 151940 Hom.: 354 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0580

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0604 AC: 9183 AN: 152058 Hom.: 355 Cov.: 32 AF XY: 0.0633 AC XY: 4707 AN XY: 74324

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0517

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0584 Hom.: 39

Bravo AF: 0.0563

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
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: rs15017; hg19: chr6-132617374;