chr17-80741808-A-G

Variant names:

• chr17-80741808-A-G
• rs9674559
• NM_020761.3:c.654+11102A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020761.3(RPTOR):​c.654+11102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,020 control chromosomes in the GnomAD database, including 3,696 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 0.22 (3696 hom., cov: 32)
• Consequence: RPTOR NM_020761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPTOR	NM_020761.3	c.654+11102A>G		intron_variant	Intron 5 of 33	ENST00000306801.8	NP_065812.1
RPTOR	NM_001163034.2	c.654+11102A>G		intron_variant	Intron 5 of 29		NP_001156506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPTOR	ENST00000306801.8	c.654+11102A>G		intron_variant	Intron 5 of 33	1	NM_020761.3	ENSP00000307272.3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33285 AN: 151902 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.219 AC: 33304 AN: 152020 Hom.: 3696 Cov.: 32 AF XY: 0.219 AC XY: 16271 AN XY: 74310

African (AFR) AF: 0.228 AC: 9432 AN: 41458

American (AMR) AF: 0.165 AC: 2526 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1012 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1021 AN: 5144

South Asian (SAS) AF: 0.216 AC: 1037 AN: 4810

European-Finnish (FIN) AF: 0.241 AC: 2545 AN: 10564

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15036 AN: 67964

Other (OTH) AF: 0.233 AC: 491 AN: 2106

Alfa AF: 0.201 Hom.: 1652

Bravo AF: 0.214

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9674559; hg19: chr17-78715608;