rs11235972
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003356.4(UCP3):c.338-96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,560,654 control chromosomes in the GnomAD database, including 45,438 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 0.21 ( 3774 hom., cov: 32)
Exomes 𝑓: 0.24 ( 41664 hom. )
Consequence
UCP3
NM_003356.4 intron
NM_003356.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.02
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UCP3 | NM_003356.4 | c.338-96C>T | intron_variant | ENST00000314032.9 | |||
UCP3 | NM_022803.3 | c.338-96C>T | intron_variant | ||||
UCP3 | XM_047427519.1 | c.338-96C>T | intron_variant | ||||
UCP3 | XR_007062495.1 | n.541-96C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UCP3 | ENST00000314032.9 | c.338-96C>T | intron_variant | 1 | NM_003356.4 | P1 | |||
UCP3 | ENST00000426995.2 | c.338-96C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.212 AC: 32246AN: 151992Hom.: 3776 Cov.: 32
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GnomAD4 exome AF: 0.239 AC: 336050AN: 1408542Hom.: 41664 Cov.: 30 AF XY: 0.239 AC XY: 166829AN XY: 697320
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GnomAD4 genome ? AF: 0.212 AC: 32246AN: 152112Hom.: 3774 Cov.: 32 AF XY: 0.217 AC XY: 16147AN XY: 74354
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3478
ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at