rs1538308

Variant names:

• chr6-132377317-G-A
• rs1538308
• NM_015529.4:c.265-2540C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-132377317-G-A
• chr6-132377317-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015529.4(MOXD1):​c.265-2540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,146 control chromosomes in the GnomAD database, including 1,821 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 0.13 (1821 hom., cov: 32)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.265-2540C>T		intron_variant	Intron 1 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.160-2540C>T		intron_variant	Intron 1 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.4-2540C>T		intron_variant	Intron 1 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.4-2540C>T		intron_variant	Intron 1 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.265-2540C>T		intron_variant	Intron 1 of 11	1	NM_015529.4	ENSP00000356940.3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19320 AN: 152028 Hom.: 1820 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19356 AN: 152146 Hom.: 1821 Cov.: 32 AF XY: 0.133 AC XY: 9876 AN XY: 74390

African (AFR) AF: 0.195 AC: 8091 AN: 41482

American (AMR) AF: 0.170 AC: 2591 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2337 AN: 5174

South Asian (SAS) AF: 0.125 AC: 605 AN: 4822

European-Finnish (FIN) AF: 0.0858 AC: 909 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0598 AC: 4067 AN: 68010

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.0951 Hom.: 473

Bravo AF: 0.137

Asia WGS AF: 0.244 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.17
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1538308; hg19: chr6-132698456;