rs7751860
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_015529.4(MOXD1):c.664-20144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00956 in 152,286 control chromosomes in the GnomAD database, including 29 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 0.0096 ( 29 hom., cov: 31)
Consequence
MOXD1
NM_015529.4 intron
NM_015529.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.268
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00956 (1456/152286) while in subpopulation AFR AF= 0.0334 (1389/41556). AF 95% confidence interval is 0.032. There are 29 homozygotes in gnomad4. There are 677 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MOXD1 | NM_015529.4 | c.664-20144A>G | intron_variant | ENST00000367963.8 | |||
MOXD1 | XM_017010714.3 | c.559-20144A>G | intron_variant | ||||
MOXD1 | XM_047418621.1 | c.403-20144A>G | intron_variant | ||||
MOXD1 | XM_047418622.1 | c.403-20144A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MOXD1 | ENST00000367963.8 | c.664-20144A>G | intron_variant | 1 | NM_015529.4 | P1 | |||
MOXD1 | ENST00000336749.3 | c.460-20144A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00950 AC: 1445AN: 152166Hom.: 29 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00956 AC: 1456AN: 152286Hom.: 29 Cov.: 31 AF XY: 0.00909 AC XY: 677AN XY: 74474
GnomAD4 genome
?
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1456
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152286
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31
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677
AN XY:
74474
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5
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at