6-132320536-T-C

Variant names:

• chr6-132320536-T-C
• rs599660
• NM_015529.4:c.1365+93A>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.1365+93A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,079,844 control chromosomes in the GnomAD database, including 101,190 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 0.51 (23826 hom., cov: 32)
  • Exomes 𝑓: 0.39 (77364 hom.)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015529.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOXD1	NM_015529.4	MANE Select	c.1365+93A>G		intron	N/A	NP_056344.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOXD1	ENST00000367963.8	TSL:1 MANE Select	c.1365+93A>G		intron	N/A	ENSP00000356940.3
	MOXD1	ENST00000336749.3	TSL:1	c.1161+93A>G		intron	N/A	ENSP00000336998.3
	MOXD1	ENST00000489128.1	TSL:3	n.487+93A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78140 AN: 151882 Hom.: 23771 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.393 AC: 364304 AN: 927844 Hom.: 77364 AF XY: 0.394 AC XY: 184873 AN XY: 468630

African (AFR) AF: 0.862 AC: 17771 AN: 20614

American (AMR) AF: 0.424 AC: 8492 AN: 20022

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 5321 AN: 18538

East Asian (EAS) AF: 0.680 AC: 21950 AN: 32290

South Asian (SAS) AF: 0.529 AC: 28737 AN: 54324

European-Finnish (FIN) AF: 0.350 AC: 15774 AN: 45096

Middle Eastern (MID) AF: 0.414 AC: 1211 AN: 2928

European-Non Finnish (NFE) AF: 0.358 AC: 247733 AN: 692846

Other (OTH) AF: 0.420 AC: 17315 AN: 41186

GnomAD4 genome AF: 0.515 AC: 78244 AN: 152000 Hom.: 23826 Cov.: 32 AF XY: 0.512 AC XY: 38056 AN XY: 74270

African (AFR) AF: 0.846 AC: 35075 AN: 41470

American (AMR) AF: 0.427 AC: 6525 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3464

East Asian (EAS) AF: 0.693 AC: 3583 AN: 5168

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3552 AN: 10536

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24455 AN: 67964

Other (OTH) AF: 0.473 AC: 997 AN: 2106

Alfa AF: 0.468 Hom.: 2612

Bravo AF: 0.536

Asia WGS AF: 0.615 AC: 2133 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-1.4
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: rs599660; hg19: chr6-132641675;