rs464921
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022551.3(RPS18):c.102+3A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,437,904 control chromosomes in the GnomAD database, including 15,267 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 ( 1277 hom., cov: 33)
Exomes 𝑓: 0.14 ( 13990 hom. )
Consequence
RPS18
NM_022551.3 splice_donor_region, intron
NM_022551.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.001239
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.364
Genes affected
RPS18 (HGNC:10401): (ribosomal protein S18) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S13P family of ribosomal proteins. It is located in the cytoplasm. The gene product of the E. coli ortholog (ribosomal protein S13) is involved in the binding of fMet-tRNA, and thus, in the initiation of translation. This gene is an ortholog of mouse Ke3. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [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=-0.54).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS18 | NM_022551.3 | c.102+3A>G | splice_donor_region_variant, intron_variant | ENST00000439602.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS18 | ENST00000439602.7 | c.102+3A>G | splice_donor_region_variant, intron_variant | 1 | NM_022551.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18162AN: 152110Hom.: 1274 Cov.: 33
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GnomAD3 exomes AF: 0.137 AC: 34572AN: 251472Hom.: 2768 AF XY: 0.145 AC XY: 19696AN XY: 135914
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GnomAD4 exome AF: 0.141 AC: 181528AN: 1285676Hom.: 13990 Cov.: 20 AF XY: 0.144 AC XY: 93642AN XY: 648366
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GnomAD4 genome ? AF: 0.119 AC: 18176AN: 152228Hom.: 1277 Cov.: 33 AF XY: 0.118 AC XY: 8791AN XY: 74436
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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
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at