17-58306816-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004758.4(TSPOAP1):āc.5136T>Cā(p.Ile1712=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00535 in 1,613,668 control chromosomes in the GnomAD database, including 415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.029 ( 207 hom., cov: 33)
Exomes š: 0.0029 ( 208 hom. )
Consequence
TSPOAP1
NM_004758.4 synonymous
NM_004758.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.919
Genes affected
TSPOAP1 (HGNC:16831): (TSPO associated protein 1) Enables benzodiazepine receptor binding activity. Predicted to be involved in regulation of presynaptic cytosolic calcium ion concentration. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 17-58306816-A-G is Benign according to our data. Variant chr17-58306816-A-G is described in ClinVar as [Benign]. Clinvar id is 789660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.919 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPOAP1 | NM_004758.4 | c.5136T>C | p.Ile1712= | synonymous_variant | 25/32 | ENST00000343736.9 | NP_004749.2 | |
TSPOAP1 | NM_001261835.2 | c.5136T>C | p.Ile1712= | synonymous_variant | 25/32 | NP_001248764.1 | ||
TSPOAP1 | NM_024418.3 | c.4956T>C | p.Ile1652= | synonymous_variant | 24/31 | NP_077729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPOAP1 | ENST00000343736.9 | c.5136T>C | p.Ile1712= | synonymous_variant | 25/32 | 1 | NM_004758.4 | ENSP00000345824 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0286 AC: 4354AN: 152086Hom.: 205 Cov.: 33
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GnomAD3 exomes AF: 0.00723 AC: 1813AN: 250600Hom.: 79 AF XY: 0.00527 AC XY: 714AN XY: 135554
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GnomAD4 exome AF: 0.00292 AC: 4264AN: 1461464Hom.: 208 Cov.: 32 AF XY: 0.00245 AC XY: 1783AN XY: 727032
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GnomAD4 genome AF: 0.0287 AC: 4368AN: 152204Hom.: 207 Cov.: 33 AF XY: 0.0274 AC XY: 2040AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 26, 2017 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at