chr20-4182190-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_175839.3(SMOX):c.711G>T(p.Ser237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 1,613,516 control chromosomes in the GnomAD database, including 245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 120 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 125 hom. )
Consequence
SMOX
NM_175839.3 synonymous
NM_175839.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.22
Genes affected
SMOX (HGNC:15862): (spermine oxidase) Polyamines are ubiquitous polycationic alkylamines which include spermine, spermidine, putrescine, and agmatine. These molecules participate in a broad range of cellular functions which include cell cycle modulation, scavenging reactive oxygen species, and the control of gene expression. These molecules also play important roles in neurotransmission through their regulation of cell-surface receptor activity, involvement in intracellular signalling pathways, and their putative roles as neurotransmitters. This gene encodes an FAD-containing enzyme that catalyzes the oxidation of spermine to spermadine and secondarily produces hydrogen peroxide. Multiple transcript variants encoding different isoenzymes have been identified for this gene, some of which have failed to demonstrate significant oxidase activity on natural polyamine substrates. The characterized isoenzymes have distinctive biochemical characteristics and substrate specificities, suggesting the existence of additional levels of complexity in polyamine catabolism. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 20-4182190-G-T is Benign according to our data. Variant chr20-4182190-G-T is described in ClinVar as [Benign]. Clinvar id is 782665.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-6.22 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOX | NM_175839.3 | c.711G>T | p.Ser237= | synonymous_variant | 5/7 | ENST00000305958.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOX | ENST00000305958.9 | c.711G>T | p.Ser237= | synonymous_variant | 5/7 | 1 | NM_175839.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0226 AC: 3441AN: 152090Hom.: 120 Cov.: 32
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GnomAD3 exomes AF: 0.00566 AC: 1416AN: 250298Hom.: 48 AF XY: 0.00385 AC XY: 521AN XY: 135490
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GnomAD4 exome AF: 0.00232 AC: 3389AN: 1461308Hom.: 125 Cov.: 37 AF XY: 0.00191 AC XY: 1389AN XY: 726994
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GnomAD4 genome ? AF: 0.0226 AC: 3439AN: 152208Hom.: 120 Cov.: 32 AF XY: 0.0218 AC XY: 1621AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at