rs113515
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000714.6(TSPO):c.183-136C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 1,066,112 control chromosomes in the GnomAD database, including 80,307 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 0.40 ( 12574 hom., cov: 33)
Exomes 𝑓: 0.37 ( 67733 hom. )
Consequence
TSPO
NM_000714.6 intron
NM_000714.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.865
Genes affected
TSPO (HGNC:1158): (translocator protein) Present mainly in the mitochondrial compartment of peripheral tissues, the protein encoded by this gene interacts with some benzodiazepines and has different affinities than its endogenous counterpart. The protein is a key factor in the flow of cholesterol into mitochondria to permit the initiation of steroid hormone synthesis. Alternatively spliced transcript variants have been reported; one of the variants lacks an internal exon and is considered non-coding, and the other variants encode the same protein. [provided by RefSeq, Feb 2012]
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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=-0.5).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPO | NM_000714.6 | c.183-136C>G | intron_variant | ENST00000337554.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPO | ENST00000337554.8 | c.183-136C>G | intron_variant | 1 | NM_000714.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.397 AC: 60283AN: 152030Hom.: 12559 Cov.: 33
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GnomAD4 exome AF: 0.374 AC: 341720AN: 913964Hom.: 67733 AF XY: 0.371 AC XY: 169254AN XY: 455710
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GnomAD4 genome ? AF: 0.397 AC: 60345AN: 152148Hom.: 12574 Cov.: 33 AF XY: 0.390 AC XY: 29027AN XY: 74380
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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