rs7211818

Variant names:

• chr17-80715103-A-G
• rs7211818
• NM_020761.3:c.507+7104A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-80715103-A-G
• chr17-80715103-A-T

Variant summary

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

The NM_020761.3(RPTOR):​c.507+7104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,234 control chromosomes in the GnomAD database, including 4,119 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 0.23 (4119 hom., cov: 34)
• Consequence: RPTOR NM_020761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967
• Publications: 22 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPTOR	NM_020761.3	c.507+7104A>G		intron_variant	Intron 4 of 33	ENST00000306801.8	NP_065812.1
RPTOR	NM_001163034.2	c.507+7104A>G		intron_variant	Intron 4 of 29		NP_001156506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPTOR	ENST00000306801.8	c.507+7104A>G		intron_variant	Intron 4 of 33	1	NM_020761.3	ENSP00000307272.3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35003 AN: 152116 Hom.: 4118 Cov.: 34

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.230 AC: 35017 AN: 152234 Hom.: 4119 Cov.: 34 AF XY: 0.233 AC XY: 17316 AN XY: 74424

African (AFR) AF: 0.232 AC: 9659 AN: 41552

American (AMR) AF: 0.172 AC: 2623 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5174

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4832

European-Finnish (FIN) AF: 0.298 AC: 3152 AN: 10594

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15103 AN: 68004

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.222 Hom.: 1948

Bravo AF: 0.222

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.92
PhyloP100		0.97
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: rs7211818; hg19: chr17-78688903;