rs3015844
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001145440.3(TYW1B):c.1370+4870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,062 control chromosomes in the GnomAD database, including 46,739 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 0.78 ( 46739 hom., cov: 31)
Consequence
TYW1B
NM_001145440.3 intron
NM_001145440.3 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.914
Genes affected
TYW1B (HGNC:33908): (tRNA-yW synthesizing protein 1 homolog B) Wybutosine is a hypermodified guanosine found in phenylalanine tRNA. Wybutosine functions to stabilize codon-anticodon interactions during ribosome decoding and therefore supports the maintenance of the reading frame. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. The human genome contains two closely related genes that putatively function in wybutosine synthesis. The open reading frame of this locus is disrupted in some individuals. Thus, this locus appears to be an evolving pseudogene, but may still be functional in some members of the population. [provided by RefSeq, Apr 2014]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYW1B | NM_001145440.3 | c.1370+4870C>T | intron_variant | ENST00000620995.5 | |||
TYW1B | NM_001412179.1 | c.1142+4870C>T | intron_variant | ||||
TYW1B | NM_001412180.1 | c.1142+4870C>T | intron_variant | ||||
TYW1B | NM_001412182.1 | c.248+4870C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYW1B | ENST00000620995.5 | c.1370+4870C>T | intron_variant | 1 | NM_001145440.3 | P1 | |||
TYW1B | ENST00000612372.4 | c.884+4870C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.779 AC: 118372AN: 151944Hom.: 46725 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.779 AC: 118418AN: 152062Hom.: 46739 Cov.: 31 AF XY: 0.776 AC XY: 57694AN XY: 74356
GnomAD4 genome
?
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at