17-80937241-C-T

Variant names:

• chr17-80937241-C-T
• rs1877926
• NM_020761.3:c.2920-3255C>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.2920-3255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,844 control chromosomes in the GnomAD database, including 10,291 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 0.37 (10291 hom., cov: 31)
• Consequence: RPTOR NM_020761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPTOR	NM_020761.3	c.2920-3255C>T		intron_variant	Intron 24 of 33	ENST00000306801.8	NP_065812.1
RPTOR	NM_001163034.2	c.2446-3255C>T		intron_variant	Intron 20 of 29		NP_001156506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPTOR	ENST00000306801.8	c.2920-3255C>T		intron_variant	Intron 24 of 33	1	NM_020761.3	ENSP00000307272.3
RPTOR	ENST00000575542.5	n.2407-3255C>T		intron_variant	Intron 20 of 29	1
RPTOR	ENST00000697423.1	c.2974-3255C>T		intron_variant	Intron 24 of 33			ENSP00000513305.1
RPTOR	ENST00000544334.6	c.2446-3255C>T		intron_variant	Intron 20 of 29	5		ENSP00000442479.2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55389 AN: 151726 Hom.: 10278 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.365 AC: 55443 AN: 151844 Hom.: 10291 Cov.: 31 AF XY: 0.361 AC XY: 26808 AN XY: 74212

African (AFR) AF: 0.410 AC: 16948 AN: 41372

American (AMR) AF: 0.347 AC: 5292 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3466

East Asian (EAS) AF: 0.475 AC: 2444 AN: 5148

South Asian (SAS) AF: 0.384 AC: 1845 AN: 4802

European-Finnish (FIN) AF: 0.272 AC: 2871 AN: 10556

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23796 AN: 67942

Other (OTH) AF: 0.361 AC: 758 AN: 2102

Alfa AF: 0.358 Hom.: 5083

Bravo AF: 0.373

Asia WGS AF: 0.436 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		0.23
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: rs1877926; hg19: chr17-78911041;