chr6-132328426-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015529.4(MOXD1):c.832A>G(p.Ile278Val) variant causes a missense change. The variant allele was found at a frequency of 0.000186 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
MOXD1
NM_015529.4 missense
NM_015529.4 missense
Scores
1
2
16
Clinical Significance
Conservation
PhyloP100: 4.97
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21748996).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MOXD1 | NM_015529.4 | c.832A>G | p.Ile278Val | missense_variant | 5/12 | ENST00000367963.8 | |
MOXD1 | XM_017010714.3 | c.727A>G | p.Ile243Val | missense_variant | 5/12 | ||
MOXD1 | XM_047418621.1 | c.571A>G | p.Ile191Val | missense_variant | 5/12 | ||
MOXD1 | XM_047418622.1 | c.571A>G | p.Ile191Val | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MOXD1 | ENST00000367963.8 | c.832A>G | p.Ile278Val | missense_variant | 5/12 | 1 | NM_015529.4 | P1 | |
MOXD1 | ENST00000336749.3 | c.628A>G | p.Ile210Val | missense_variant | 4/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152116Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251222Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135770
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GnomAD4 exome AF: 0.000188 AC: 275AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.000194 AC XY: 141AN XY: 727226
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GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74314
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.832A>G (p.I278V) alteration is located in exon 5 (coding exon 5) of the MOXD1 gene. This alteration results from a A to G substitution at nucleotide position 832, causing the isoleucine (I) at amino acid position 278 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Pathogenic
D;D
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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