rs927450
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_037166.1(SOD2-OT1):n.912T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 153,446 control chromosomes in the GnomAD database, including 18,128 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 0.46 ( 17953 hom., cov: 32)
Exomes 𝑓: 0.43 ( 175 hom. )
Consequence
SOD2-OT1
NR_037166.1 non_coding_transcript_exon
NR_037166.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.150
Genes affected
SOD2-OT1 (HGNC:53445): (SOD2 overlapping transcript 1)
SOD2 (HGNC:11180): (superoxide dismutase 2) This gene is a member of the iron/manganese superoxide dismutase family. It encodes a mitochondrial protein that forms a homotetramer and binds one manganese ion per subunit. This protein binds to the superoxide byproducts of oxidative phosphorylation and converts them to hydrogen peroxide and diatomic oxygen. Mutations in this gene have been associated with idiopathic cardiomyopathy (IDC), premature aging, sporadic motor neuron disease, and cancer. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 1. [provided by RefSeq, Apr 2016]
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOD2-OT1 | NR_037166.1 | n.912T>C | non_coding_transcript_exon_variant | 2/2 | |||
SOD2 | NM_001322817.2 | c.-363T>C | 5_prime_UTR_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOD2-OT1 | ENST00000535372.1 | n.912T>C | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
SOD2 | ENST00000546087.5 | c.-363T>C | 5_prime_UTR_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.456 AC: 69283AN: 151944Hom.: 17947 Cov.: 32
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GnomAD4 exome AF: 0.434 AC: 601AN: 1384Hom.: 175 Cov.: 0 AF XY: 0.441 AC XY: 377AN XY: 854
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GnomAD4 genome ? AF: 0.456 AC: 69282AN: 152062Hom.: 17953 Cov.: 32 AF XY: 0.454 AC XY: 33755AN XY: 74322
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ClinVar
Not reported inComputational scores
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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