NM_178526.5:c.81+103T>C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178526.5(SLC25A42):c.81+103T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000162 in 618,442 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC25A42
NM_178526.5 intron
NM_178526.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
SLC25A42 (HGNC:28380): (solute carrier family 25 member 42) This gene encodes a solute carrier family 25 protein. Solute carrier family 25 proteins are localized to mitochondria and play critical roles in the transport of molecules across the inner mitochondrial membrane. The encoded protein is a mitochondrial transporter for coenzyme A (CoA) and adenosine 3',5'-diphosphate. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A42 | NM_178526.5 | c.81+103T>C | intron_variant | Intron 2 of 7 | ENST00000318596.8 | NP_848621.2 | ||
SLC25A42 | NM_001321544.2 | c.81+103T>C | intron_variant | Intron 2 of 7 | NP_001308473.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A42 | ENST00000318596.8 | c.81+103T>C | intron_variant | Intron 2 of 7 | 1 | NM_178526.5 | ENSP00000326693.6 | |||
SLC25A42 | ENST00000594070.5 | n.263+103T>C | intron_variant | Intron 1 of 4 | 2 | |||||
SLC25A42 | ENST00000597661.5 | n.144+103T>C | intron_variant | Intron 2 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 27952Hom.: 0 Cov.: 0 FAILED QC
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GnomAD4 exome AF: 0.00000162 AC: 1AN: 618442Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 318840
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 27952Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 13670
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Data not reliable, filtered out with message: AC0;AS_VQSR
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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