rs17316227
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033284.2(TBL1Y):c.59-4947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.059 ( 0 hom., 2010 hem., cov: 0)
Consequence
TBL1Y
NM_033284.2 intron
NM_033284.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.543
Genes affected
TBL1Y (HGNC:18502): (transducin beta like 1 Y-linked) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This gene is highly similar to TBL1X gene in nucleotide sequence and protein sequence, but the TBL1X gene is located on chromosome X and this gene is on chromosome Y. This gene has three alternatively spliced transcript variants encoding the same protein. [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=-0.97).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBL1Y | NM_033284.2 | c.59-4947A>G | intron_variant | ENST00000383032.6 | |||
TBL1Y | NM_134258.2 | c.59-4947A>G | intron_variant | ||||
TBL1Y | NM_134259.2 | c.59-4947A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBL1Y | ENST00000383032.6 | c.59-4947A>G | intron_variant | 1 | NM_033284.2 | P1 | |||
TBL1Y | ENST00000346432.3 | c.59-4947A>G | intron_variant | 1 | P1 | ||||
TBL1Y | ENST00000355162.6 | c.59-4947A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0593 AC: 2011AN: 33923Hom.: 0 Cov.: 0 AF XY: 0.0593 AC XY: 2011AN XY: 33923
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GnomAD4 genome ? AF: 0.0591 AC: 2010AN: 33987Hom.: 0 Cov.: 0 AF XY: 0.0591 AC XY: 2010AN XY: 33987
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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