rs9897968

Variant names:

• chr17-80920714-G-A
• rs9897968
• NM_020761.3:c.2521-2010G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-80920714-G-A
• chr17-80920714-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020761.3(RPTOR):​c.2521-2010G>A 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 152,262 control chromosomes in the GnomAD database, including 4,621 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 (4621 hom., cov: 34)
• Consequence: RPTOR NM_020761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPTOR	NM_020761.3	c.2521-2010G>A		intron_variant	Intron 21 of 33	ENST00000306801.8	NP_065812.1
RPTOR	NM_001163034.2	c.2047-2010G>A		intron_variant	Intron 17 of 29		NP_001156506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPTOR	ENST00000306801.8	c.2521-2010G>A		intron_variant	Intron 21 of 33	1	NM_020761.3	ENSP00000307272.3
RPTOR	ENST00000575542.5	n.2008-2010G>A		intron_variant	Intron 17 of 29	1
RPTOR	ENST00000697423.1	c.2575-2010G>A		intron_variant	Intron 21 of 33			ENSP00000513305.1
RPTOR	ENST00000544334.6	c.2047-2010G>A		intron_variant	Intron 17 of 29	5		ENSP00000442479.2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36052 AN: 152142 Hom.: 4608 Cov.: 34

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.220

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.237 AC: 36097 AN: 152262 Hom.: 4621 Cov.: 34 AF XY: 0.234 AC XY: 17427 AN XY: 74450

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.217

Alfa AF: 0.201 Hom.: 4417

Bravo AF: 0.243

Asia WGS AF: 0.100 AC: 348 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	0.89
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs9897968; hg19: chr17-78894514; COSMIC: COSV60820899; COSMIC: COSV60820899;