rs2289759
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_020761.3(RPTOR):āc.1518A>Gā(p.Gln506=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,612,836 control chromosomes in the GnomAD database, including 54,709 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 0.23 ( 4096 hom., cov: 32)
Exomes š: 0.26 ( 50613 hom. )
Consequence
RPTOR
NM_020761.3 synonymous
NM_020761.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.857
Genes affected
RPTOR (HGNC:30287): (regulatory associated protein of MTOR complex 1) This gene encodes a component of a signaling pathway that regulates cell growth in response to nutrient and insulin levels. The encoded protein forms a stoichiometric complex with the mTOR kinase, and also associates with eukaryotic initiation factor 4E-binding protein-1 and ribosomal protein S6 kinase. The protein positively regulates the downstream effector ribosomal protein S6 kinase, and negatively regulates the mTOR kinase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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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=-0.6).
BP7
Synonymous conserved (PhyloP=-0.857 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPTOR | NM_020761.3 | c.1518A>G | p.Gln506= | synonymous_variant | 14/34 | ENST00000306801.8 | NP_065812.1 | |
RPTOR | NM_001163034.2 | c.1510-11297A>G | intron_variant | NP_001156506.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPTOR | ENST00000306801.8 | c.1518A>G | p.Gln506= | synonymous_variant | 14/34 | 1 | NM_020761.3 | ENSP00000307272 | P1 |
Frequencies
GnomAD3 genomes AF: 0.226 AC: 34373AN: 152032Hom.: 4092 Cov.: 32
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GnomAD3 exomes AF: 0.258 AC: 64765AN: 251220Hom.: 8787 AF XY: 0.259 AC XY: 35189AN XY: 135844
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GnomAD4 exome AF: 0.260 AC: 380484AN: 1460686Hom.: 50613 Cov.: 33 AF XY: 0.261 AC XY: 189433AN XY: 726686
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GnomAD4 genome AF: 0.226 AC: 34392AN: 152150Hom.: 4096 Cov.: 32 AF XY: 0.226 AC XY: 16845AN XY: 74388
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at