rs12602885
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020761.3(RPTOR):c.-261G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 352,010 control chromosomes in the GnomAD database, including 6,889 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 0.16 ( 2352 hom., cov: 32)
Exomes 𝑓: 0.20 ( 4537 hom. )
Consequence
RPTOR
NM_020761.3 5_prime_UTR
NM_020761.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.780
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPTOR | NM_020761.3 | c.-261G>A | 5_prime_UTR_variant | 1/34 | ENST00000306801.8 | ||
RPTOR | NM_001163034.2 | c.-261G>A | 5_prime_UTR_variant | 1/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPTOR | ENST00000306801.8 | c.-261G>A | 5_prime_UTR_variant | 1/34 | 1 | NM_020761.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.165 AC: 25053AN: 152068Hom.: 2351 Cov.: 32
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GnomAD4 exome AF: 0.204 AC: 40675AN: 199824Hom.: 4537 Cov.: 0 AF XY: 0.203 AC XY: 20608AN XY: 101618
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GnomAD4 genome ? AF: 0.165 AC: 25062AN: 152186Hom.: 2352 Cov.: 32 AF XY: 0.165 AC XY: 12285AN XY: 74388
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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