Genetic Variant MOXD1:c.1365+93A>G (chr6-132320536-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

2 publications found

Variant links:

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]

MOXD1 links:

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ACMG classification

Classification was made for transcript

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

Sel.	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	Q6UVY6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MOXD1	ENST00000367963.8	TSL:1 MANE Select	c.1365+93A>G	intron	N/A	ENSP00000356940.3	Q6UVY6-1
MOXD1	ENST00000336749.3	TSL:1	c.1161+93A>G	intron	N/A	ENSP00000336998.3	Q6UVY6-2
MOXD1	ENST00000940886.1		c.1353+93A>G	intron	N/A	ENSP00000610945.1

Frequencies

GnomAD3 genomes

AF:

0.514

AC:

78140

AN:

151882

Hom.:

23771

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

9922

19844

29765

39687

49609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7086

14172

21258

28344

35430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.515

AC:

78244

AN:

152000

Hom.:

23826

Cov.:

AF XY:

0.512

AC XY:

38056

AN XY:

74270

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1546

3092

4637

6183

7729

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.74

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over