rs3734744

Variant names:

• chr6-132374877-T-A
• ENST00000336749.3:c.-40A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-132374877-T-A
• chr6-132374877-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42

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

Verdict is Likely_benign. Variant got -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.265-100A>T		intron_variant	Intron 1 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.160-100A>T		intron_variant	Intron 1 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.4-100A>T		intron_variant	Intron 1 of 11		XP_047274577.1
MOXD1	XM_047418622.1	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	c.-40A>T		5_prime_UTR_variant	Exon 1 of 11	1		ENSP00000336998.3
MOXD1	ENST00000367963.8	c.265-100A>T		intron_variant	Intron 1 of 11	1	NM_015529.4	ENSP00000356940.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 9.41e-7 AC: 1 AN: 1063162 Hom.: 0 Cov.: 14 AF XY: 0.00000187 AC XY: 1 AN XY: 536182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000149

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

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
DANN	Benign	0.49

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-132696016;