19-54190237-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000455798.6(TSEN34):c.-5+75C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0232 in 881,616 control chromosomes in the GnomAD database, including 681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.045 ( 298 hom., cov: 34)
Exomes 𝑓: 0.019 ( 383 hom. )
Consequence
TSEN34
ENST00000455798.6 intron
ENST00000455798.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.52
Genes affected
TSEN34 (HGNC:15506): (tRNA splicing endonuclease subunit 34) This gene encodes a catalytic subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from precursor tRNAs. The endonuclease complex is also associated with a pre-mRNA 3-prime end processing factor. A mutation in this gene results in the neurological disorder pontocerebellar hypoplasia type 2. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 19-54190237-C-T is Benign according to our data. Variant chr19-54190237-C-T is described in ClinVar as [Benign]. Clinvar id is 1236557.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSEN34 | XM_011527294.4 | c.-5+75C>T | intron_variant | ||||
TSEN34 | XM_047439391.1 | c.-5+641C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSEN34 | ENST00000455798.6 | c.-5+75C>T | intron_variant | 2 | P2 | ||||
TSEN34 | ENST00000302937.8 | upstream_gene_variant | 1 | P2 | |||||
TSEN34 | ENST00000429671.7 | upstream_gene_variant | 2 | P2 | |||||
TSEN34 | ENST00000667261.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0452 AC: 6868AN: 151872Hom.: 299 Cov.: 34
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GnomAD4 exome AF: 0.0187 AC: 13622AN: 729624Hom.: 383 Cov.: 10 AF XY: 0.0177 AC XY: 6694AN XY: 377982
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GnomAD4 genome ? AF: 0.0452 AC: 6873AN: 151992Hom.: 298 Cov.: 34 AF XY: 0.0457 AC XY: 3392AN XY: 74300
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at