rs17628
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000251453.8(RPS16):āc.27T>Gā(p.Ser9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,607,704 control chromosomes in the GnomAD database, including 115,015 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: š 0.44 ( 16482 hom., cov: 33)
Exomes š: 0.36 ( 98533 hom. )
Consequence
RPS16
ENST00000251453.8 synonymous
ENST00000251453.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.377
Genes affected
RPS16 (HGNC:10396): (ribosomal protein S16) 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 S9P family of ribosomal proteins. It is located in the cytoplasm. 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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-0.377 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS16 | NM_001020.6 | c.27T>G | p.Ser9= | synonymous_variant | 1/5 | ENST00000251453.8 | NP_001011.1 | |
RPS16 | NM_001363860.2 | c.27T>G | p.Ser9= | synonymous_variant | 1/4 | NP_001350789.1 | ||
RPS16 | NM_001321111.2 | c.27T>G | p.Ser9= | synonymous_variant | 1/5 | NP_001308040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS16 | ENST00000251453.8 | c.27T>G | p.Ser9= | synonymous_variant | 1/5 | 1 | NM_001020.6 | ENSP00000251453 | P1 |
Frequencies
GnomAD3 genomes AF: 0.445 AC: 67569AN: 151928Hom.: 16451 Cov.: 33
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GnomAD3 exomes AF: 0.391 AC: 96413AN: 246842Hom.: 19925 AF XY: 0.386 AC XY: 51752AN XY: 133918
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GnomAD4 exome AF: 0.363 AC: 527927AN: 1455660Hom.: 98533 Cov.: 41 AF XY: 0.364 AC XY: 263609AN XY: 724570
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GnomAD4 genome AF: 0.445 AC: 67644AN: 152044Hom.: 16482 Cov.: 33 AF XY: 0.445 AC XY: 33065AN XY: 74314
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ClinVar
Not reported inComputational scores
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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