11-74001663-G-GTC
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003356.4(UCP3):c.825-139_825-138dupGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 711,692 control chromosomes in the GnomAD database, including 7,691 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2494 hom., cov: 28)
Exomes 𝑓: 0.15 ( 5197 hom. )
Consequence
UCP3
NM_003356.4 intron
NM_003356.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.517
Genes affected
UCP3 (HGNC:12519): (uncoupling protein 3) Mitochondrial uncoupling proteins (UCP) are members of the larger family of mitochondrial anion carrier proteins (MACP). UCPs separate oxidative phosphorylation from ATP synthesis with energy dissipated as heat, also referred to as the mitochondrial proton leak. UCPs facilitate the transfer of anions from the inner to the outer mitochondrial membrane and the return transfer of protons from the outer to the inner mitochondrial membrane. They also reduce the mitochondrial membrane potential in mammalian cells. The different UCPs have tissue-specific expression; this gene is primarily expressed in skeletal muscle. This gene's protein product is postulated to protect mitochondria against lipid-induced oxidative stress. Expression levels of this gene increase when fatty acid supplies to mitochondria exceed their oxidation capacity and the protein enables the export of fatty acids from mitochondria. UCPs contain the three solcar protein domains typically found in MACPs. Two splice variants have been found for this gene.[provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 11-74001663-G-GTC is Benign according to our data. Variant chr11-74001663-G-GTC is described in ClinVar as [Benign]. Clinvar id is 1286622.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UCP3 | NM_003356.4 | c.825-139_825-138dupGA | intron_variant | ENST00000314032.9 | NP_003347.1 | |||
UCP3 | XM_047427519.1 | c.825-139_825-138dupGA | intron_variant | XP_047283475.1 | ||||
UCP3 | XR_007062495.1 | n.3114+75_3114+76dupGA | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UCP3 | ENST00000314032.9 | c.825-139_825-138dupGA | intron_variant | 1 | NM_003356.4 | ENSP00000323740.4 | ||||
UCP3 | ENST00000545271.1 | n.515+75_515+76dupGA | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25072AN: 148208Hom.: 2492 Cov.: 28
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GnomAD4 exome AF: 0.153 AC: 85957AN: 563386Hom.: 5197 Cov.: 7 AF XY: 0.149 AC XY: 44601AN XY: 298658
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GnomAD4 genome AF: 0.169 AC: 25076AN: 148306Hom.: 2494 Cov.: 28 AF XY: 0.166 AC XY: 12006AN XY: 72314
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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 | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at