rs2275716
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152707.4(SLC25A16):c.224-71C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 925,650 control chromosomes in the GnomAD database, including 294,079 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 0.73 ( 41900 hom., cov: 32)
Exomes 𝑓: 0.80 ( 252179 hom. )
Consequence
SLC25A16
NM_152707.4 intron
NM_152707.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.227
Genes affected
SLC25A16 (HGNC:10986): (solute carrier family 25 member 16) This gene encodes a protein that contains three tandemly repeated mitochondrial carrier protein domains. The encoded protein is localized in the inner membrane and facilitates the rapid transport and exchange of molecules between the cytosol and the mitochondrial matrix space. This gene has a possible role in Graves' disease. [provided by RefSeq, Jul 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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A16 | NM_152707.4 | c.224-71C>A | intron_variant | ENST00000609923.6 | NP_689920.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A16 | ENST00000609923.6 | c.224-71C>A | intron_variant | 1 | NM_152707.4 | ENSP00000476815.1 | ||||
SLC25A16 | ENST00000493963.5 | n.*152-71C>A | intron_variant | 1 | ENSP00000476283.1 | |||||
SLC25A16 | ENST00000265870.7 | n.1229-71C>A | intron_variant | 2 | ||||||
SLC25A16 | ENST00000491102.2 | n.*127-71C>A | intron_variant | 4 | ENSP00000476555.1 |
Frequencies
GnomAD3 genomes AF: 0.733 AC: 111381AN: 151926Hom.: 41901 Cov.: 32
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GnomAD4 exome AF: 0.805 AC: 622455AN: 773606Hom.: 252179 AF XY: 0.800 AC XY: 316708AN XY: 395740
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GnomAD4 genome AF: 0.733 AC: 111401AN: 152044Hom.: 41900 Cov.: 32 AF XY: 0.731 AC XY: 54335AN XY: 74316
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at