rs6937164

Variant names:

• chr6-132374173-A-G
• rs6937164
• NM_015529.4:c.411+458T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-132374173-A-G
• chr6-132374173-A-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.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
• Publications: 3 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=-0.9).
• 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 rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.411+458T>C		intron_variant	Intron 2 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.306+458T>C		intron_variant	Intron 2 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.150+458T>C		intron_variant	Intron 2 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.150+458T>C		intron_variant	Intron 2 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.411+458T>C		intron_variant	Intron 2 of 11	1	NM_015529.4	ENSP00000356940.3
MOXD1	ENST00000336749.3	c.207+458T>C		intron_variant	Intron 1 of 10	1		ENSP00000336998.3

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

African (AFR) AF: 0.845 AC: 35085 AN: 41516

American (AMR) AF: 0.389 AC: 5928 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1059 AN: 3466

East Asian (EAS) AF: 0.697 AC: 3610 AN: 5176

South Asian (SAS) AF: 0.393 AC: 1892 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2383 AN: 10574

Middle Eastern (MID) AF: 0.413 AC: 119 AN: 288

European-Non Finnish (NFE) AF: 0.239 AC: 16236 AN: 67974

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.314 Hom.: 20847

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
PhyloP100		-0.46
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: rs6937164; hg19: chr6-132695312;