rs9381469
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004277.5(SLC25A27):c.384-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,589,822 control chromosomes in the GnomAD database, including 185,202 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 0.48 ( 17850 hom., cov: 31)
Exomes 𝑓: 0.48 ( 167352 hom. )
Consequence
SLC25A27
NM_004277.5 intron
NM_004277.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0250
Genes affected
SLC25A27 (HGNC:21065): (solute carrier family 25 member 27) 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. Tissue specificity occurs for the different UCPs and the exact methods of how UCPs transfer H+/OH- are not known. UCPs contain the three homologous protein domains of MACPs. Transcripts of this gene are only detected in brain tissue and are specifically modulated by various environmental conditions. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2011]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A27 | NM_004277.5 | c.384-45G>A | intron_variant | ENST00000371347.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A27 | ENST00000371347.10 | c.384-45G>A | intron_variant | 1 | NM_004277.5 | P1 | |||
SLC25A27 | ENST00000411689.6 | c.384-45G>A | intron_variant | 1 | |||||
SLC25A27 | ENST00000603486.5 | c.174-45G>A | intron_variant | 5 | |||||
SLC25A27 | ENST00000604908.1 | n.295-45G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.484 AC: 73402AN: 151786Hom.: 17843 Cov.: 31
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GnomAD3 exomes AF: 0.456 AC: 111487AN: 244736Hom.: 26145 AF XY: 0.448 AC XY: 59429AN XY: 132798
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GnomAD4 exome AF: 0.478 AC: 687492AN: 1437918Hom.: 167352 Cov.: 26 AF XY: 0.472 AC XY: 338408AN XY: 716352
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GnomAD4 genome ? AF: 0.484 AC: 73452AN: 151904Hom.: 17850 Cov.: 31 AF XY: 0.480 AC XY: 35642AN XY: 74218
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ClinVar
Not reported inComputational scores
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Name
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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