rs11256802
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032905.5(RBM17):c.506-148A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 555,128 control chromosomes in the GnomAD database, including 2,674 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 0.094 ( 745 hom., cov: 31)
Exomes 𝑓: 0.090 ( 1929 hom. )
Consequence
RBM17
NM_032905.5 intron
NM_032905.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.629
Genes affected
RBM17 (HGNC:16944): (RNA binding motif protein 17) This gene encodes an RNA binding protein. The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 9 and 15. [provided by RefSeq, Mar 2009]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM17 | NM_032905.5 | c.506-148A>C | intron_variant | ENST00000379888.9 | |||
RBM17 | NM_001145547.2 | c.506-148A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM17 | ENST00000379888.9 | c.506-148A>C | intron_variant | 1 | NM_032905.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0944 AC: 14336AN: 151924Hom.: 744 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.0900 AC: 36278AN: 403086Hom.: 1929 Cov.: 5 AF XY: 0.0895 AC XY: 19031AN XY: 212592
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GnomAD4 genome ? AF: 0.0944 AC: 14354AN: 152042Hom.: 745 Cov.: 31 AF XY: 0.0953 AC XY: 7085AN XY: 74332
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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