rs12530
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014306.5(RTCB):c.*75A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 979,458 control chromosomes in the GnomAD database, including 13,715 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 0.12 ( 1576 hom., cov: 33)
Exomes 𝑓: 0.16 ( 12139 hom. )
Consequence
RTCB
NM_014306.5 3_prime_UTR
NM_014306.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.485
Genes affected
RTCB (HGNC:26935): (RNA 2',3'-cyclic phosphate and 5'-OH ligase) Enables RNA ligase (ATP) activity and vinculin binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Located in cytosol and nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTCB | NM_014306.5 | c.*75A>G | 3_prime_UTR_variant | 12/12 | ENST00000216038.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTCB | ENST00000216038.6 | c.*75A>G | 3_prime_UTR_variant | 12/12 | 1 | NM_014306.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.124 AC: 18935AN: 152188Hom.: 1575 Cov.: 33
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GnomAD4 exome AF: 0.159 AC: 131416AN: 827152Hom.: 12139 Cov.: 11 AF XY: 0.155 AC XY: 67378AN XY: 433650
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GnomAD4 genome ? AF: 0.124 AC: 18936AN: 152306Hom.: 1576 Cov.: 33 AF XY: 0.123 AC XY: 9160AN XY: 74468
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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
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