6-132299855-T-C

Variant names:

• chr6-132299855-T-C
• rs2206064
• NM_015529.4:c.1509-1900A>G

Variant summary

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

The NM_015529.4(MOXD1):​c.1509-1900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 151,954 control chromosomes in the GnomAD database, including 609 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 0.056 (609 hom., cov: 31)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.1509-1900A>G		intron_variant	Intron 10 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.1404-1900A>G		intron_variant	Intron 10 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.1248-1900A>G		intron_variant	Intron 10 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.1248-1900A>G		intron_variant	Intron 10 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.1509-1900A>G		intron_variant	Intron 10 of 11	1	NM_015529.4	ENSP00000356940.3
MOXD1	ENST00000336749.3	c.1305-1900A>G		intron_variant	Intron 9 of 10	1		ENSP00000336998.3

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8456 AN: 151838 Hom.: 608 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.00917

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00706

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0558 AC: 8480 AN: 151954 Hom.: 609 Cov.: 31 AF XY: 0.0570 AC XY: 4235 AN XY: 74268

African (AFR) AF: 0.113 AC: 4698 AN: 41456

American (AMR) AF: 0.0719 AC: 1097 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1712 AN: 5128

South Asian (SAS) AF: 0.0473 AC: 227 AN: 4798

European-Finnish (FIN) AF: 0.00917 AC: 97 AN: 10580

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00705 AC: 479 AN: 67954

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0330 Hom.: 27

Bravo AF: 0.0676

Asia WGS AF: 0.145 AC: 500 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.49
PhyloP100		-2.5
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: rs2206064; hg19: chr6-132620994;