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GeneBe

rs4889863

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020761.3(RPTOR):​c.162+30877A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,154 control chromosomes in the GnomAD database, including 5,289 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 0.24 ( 5289 hom., cov: 33)

Consequence

RPTOR
NM_020761.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115
Variant links:
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPTORNM_020761.3 linkuse as main transcriptc.162+30877A>G intron_variant ENST00000306801.8
LOC105371922XR_007065932.1 linkuse as main transcriptn.302+3136T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPTORENST00000306801.8 linkuse as main transcriptc.162+30877A>G intron_variant 1 NM_020761.3 P1Q8N122-1

Frequencies

GnomAD3 genomes
AF:
0.237
AC:
36016
AN:
152036
Hom.:
5272
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0838
Gnomad AMI
AF:
0.345
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.201
Gnomad EAS
AF:
0.418
Gnomad SAS
AF:
0.384
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.256
Gnomad OTH
AF:
0.226
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.237
AC:
36047
AN:
152154
Hom.:
5289
Cov.:
33
AF XY:
0.246
AC XY:
18319
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0836
Gnomad4 AMR
AF:
0.391
Gnomad4 ASJ
AF:
0.201
Gnomad4 EAS
AF:
0.419
Gnomad4 SAS
AF:
0.383
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.256
Gnomad4 OTH
AF:
0.231
Alfa
AF:
0.255
Hom.:
2963
Bravo
AF:
0.236
Asia WGS
AF:
0.405
AC:
1404
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.1
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4889863; hg19: chr17-78550468; API