chr1-184051999-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_052965.4(TSEN15):c.135+109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,159,872 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 23 hom., cov: 32)
Exomes 𝑓: 0.00096 ( 17 hom. )
Consequence
TSEN15
NM_052965.4 intron
NM_052965.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.293
Genes affected
TSEN15 (HGNC:16791): (tRNA splicing endonuclease subunit 15) This gene encodes a subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from tRNA precursors. Alternative splicing results in multiple transcript variants. There is a pseudogene of this gene on chromosome 17. [provided by RefSeq, Jul 2014]
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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=-0.77).
BP6
?
Variant 1-184051999-C-T is Benign according to our data. Variant chr1-184051999-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317866.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.01 (1529/152286) while in subpopulation AFR AF= 0.0351 (1458/41544). AF 95% confidence interval is 0.0336. There are 23 homozygotes in gnomad4. There are 713 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSEN15 | NM_052965.4 | c.135+109C>T | intron_variant | ENST00000645668.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSEN15 | ENST00000645668.2 | c.135+109C>T | intron_variant | NM_052965.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0100 AC: 1528AN: 152168Hom.: 23 Cov.: 32
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GnomAD4 exome AF: 0.000964 AC: 971AN: 1007586Hom.: 17 AF XY: 0.000837 AC XY: 405AN XY: 484132
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GnomAD4 genome ? AF: 0.0100 AC: 1529AN: 152286Hom.: 23 Cov.: 32 AF XY: 0.00957 AC XY: 713AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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