5-135842435-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001349336.2(SLC25A48):āc.66T>Cā(p.Val22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 1,611,370 control chromosomes in the GnomAD database, including 524,155 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: š 0.78 ( 46647 hom., cov: 32)
Exomes š: 0.81 ( 477508 hom. )
Consequence
SLC25A48
NM_001349336.2 synonymous
NM_001349336.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.66
Genes affected
SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=-2.66 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A48 | NM_001349336.2 | c.66T>C | p.Val22= | synonymous_variant | 2/8 | ENST00000681962.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A48 | ENST00000681962.1 | c.66T>C | p.Val22= | synonymous_variant | 2/8 | NM_001349336.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.781 AC: 118755AN: 152004Hom.: 46611 Cov.: 32
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GnomAD3 exomes AF: 0.764 AC: 190457AN: 249416Hom.: 74029 AF XY: 0.774 AC XY: 104813AN XY: 135338
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GnomAD4 exome AF: 0.807 AC: 1177191AN: 1459248Hom.: 477508 Cov.: 48 AF XY: 0.808 AC XY: 586557AN XY: 726018
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GnomAD4 genome AF: 0.781 AC: 118841AN: 152122Hom.: 46647 Cov.: 32 AF XY: 0.779 AC XY: 57944AN XY: 74368
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at