rs599660

Variant names:

• chr6-132320536-T-A
• NM_015529.4:c.1365+93A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-132320536-T-A
• chr6-132320536-T-C
• chr6-132320536-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015529.4(MOXD1):​c.1365+93A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000107 in 930,556 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: 32)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: MOXD1 NM_015529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOXD1	NM_015529.4	c.1365+93A>T		intron_variant	Intron 9 of 11	ENST00000367963.8	NP_056344.2
MOXD1	XM_017010714.3	c.1260+93A>T		intron_variant	Intron 9 of 11		XP_016866203.1
MOXD1	XM_047418621.1	c.1104+93A>T		intron_variant	Intron 9 of 11		XP_047274577.1
MOXD1	XM_047418622.1	c.1104+93A>T		intron_variant	Intron 9 of 11		XP_047274578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOXD1	ENST00000367963.8	c.1365+93A>T		intron_variant	Intron 9 of 11	1	NM_015529.4	ENSP00000356940.3
MOXD1	ENST00000336749.3	c.1161+93A>T		intron_variant	Intron 8 of 10	1		ENSP00000336998.3
MOXD1	ENST00000489128.1	n.487+93A>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000107 AC: 1 AN: 930556 Hom.: 0 AF XY: 0.00000213 AC XY: 1 AN XY: 469994

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000498

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr6-132641675;