rs57636645
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_207346.3(TSEN54):c.521+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,610,374 control chromosomes in the GnomAD database, including 1,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.060 ( 883 hom., cov: 32)
Exomes 𝑓: 0.0066 ( 851 hom. )
Consequence
TSEN54
NM_207346.3 intron
NM_207346.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0350
Genes affected
TSEN54 (HGNC:27561): (tRNA splicing endonuclease subunit 54) This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 17-75519086-C-T is Benign according to our data. Variant chr17-75519086-C-T is described in ClinVar as [Benign]. Clinvar id is 160135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSEN54 | NM_207346.3 | c.521+39C>T | intron_variant | ENST00000333213.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSEN54 | ENST00000333213.11 | c.521+39C>T | intron_variant | 1 | NM_207346.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0602 AC: 9146AN: 151910Hom.: 879 Cov.: 32
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GnomAD3 exomes AF: 0.0165 AC: 4145AN: 251488Hom.: 372 AF XY: 0.0121 AC XY: 1647AN XY: 135916
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GnomAD4 exome AF: 0.00659 AC: 9604AN: 1458346Hom.: 851 Cov.: 32 AF XY: 0.00569 AC XY: 4131AN XY: 725740
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GnomAD4 genome ? AF: 0.0603 AC: 9164AN: 152028Hom.: 883 Cov.: 32 AF XY: 0.0584 AC XY: 4338AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2018 | - - |
Computational 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