Genetic Variant MOXD1:c.-40A>T (chr6-132374877-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000336749.3(MOXD1):c.-40A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000941 in 1,063,162 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 9.4e-7 ( 0 hom. )

Consequence

MOXD1
ENST00000336749.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.42

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4 link	c.265-100A>T	intron_variant	Intron 1 of 11	ENST00000367963.8	NP_056344.2	Q6UVY6-1
MOXD1	XM_017010714.3 link	c.160-100A>T	intron_variant	Intron 1 of 11		XP_016866203.1
MOXD1	XM_047418621.1 link	c.4-100A>T	intron_variant	Intron 1 of 11		XP_047274577.1
MOXD1	XM_047418622.1 link	c.4-100A>T	intron_variant	Intron 1 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000336749.3 link	c.-40A>T		5_prime_UTR_variant	Exon 1 of 11	1		ENSP00000336998.3		Q6UVY6-2
MOXD1	ENST00000367963.8 link	c.265-100A>T		intron_variant	Intron 1 of 11	1	NM_015529.4	ENSP00000356940.3		Q6UVY6-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.41e-7

AC:

AN:

1063162

Hom.:

Cov.:

AF XY:

0.00000187

AC XY:

AN XY:

536182

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23996

American (AMR)

AF:

0.00

AC:

AN:

30596

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21422

East Asian (EAS)

AF:

0.00

AC:

AN:

34354

South Asian (SAS)

AF:

0.0000149

AC:

AN:

67204

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45312

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3478

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

790298

Other (OTH)

AF:

0.00

AC:

AN:

46502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.7

(source)

DANN

Benign

0.49

PhyloP100

2.4

PromoterAI

0.0054

Neutral

(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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over