rs760477
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013432.5(TONSL):c.448+78C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 1,474,222 control chromosomes in the GnomAD database, including 159,132 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 0.41 ( 13582 hom., cov: 34)
Exomes 𝑓: 0.47 ( 145550 hom. )
Consequence
TONSL
NM_013432.5 intron
NM_013432.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.12
Genes affected
TONSL (HGNC:7801): (tonsoku like, DNA repair protein) The protein encoded by this gene is thought to be a negative regulator of NF-kappa-B mediated transcription. The encoded protein may bind NF-kappa-B complexes and trap them in the cytoplasm, preventing them from entering the nucleus and interacting with the DNA. Phosphorylation of this protein targets it for degradation by the ubiquitination pathway, which frees the NF-kappa-B complexes to enter the nucleus. [provided by RefSeq, Jul 2008]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TONSL | NM_013432.5 | c.448+78C>T | intron_variant | ENST00000409379.8 | |||
TONSL | XM_011517050.3 | c.448+78C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TONSL | ENST00000409379.8 | c.448+78C>T | intron_variant | 1 | NM_013432.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.414 AC: 62928AN: 152058Hom.: 13589 Cov.: 34
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GnomAD4 exome AF: 0.466 AC: 615729AN: 1322046Hom.: 145550 Cov.: 23 AF XY: 0.469 AC XY: 303211AN XY: 646686
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GnomAD4 genome ? AF: 0.414 AC: 62939AN: 152176Hom.: 13582 Cov.: 34 AF XY: 0.416 AC XY: 30974AN XY: 74404
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at