rs13160161

Variant names:

• chr5-39058254-G-A
• rs13160161
• NM_152756.5:c.97+15857C>T

Variant summary

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

The NM_152756.5(RICTOR):​c.97+15857C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,686 control chromosomes in the GnomAD database, including 10,820 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 (10820 hom., cov: 32)
• Consequence: RICTOR NM_152756.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 9 publications found

Genes affected

RICTOR (HGNC:28611): (RPTOR independent companion of MTOR complex 2) RICTOR and MTOR (FRAP1; MIM 601231) are components of a protein complex that integrates nutrient- and growth factor-derived signals to regulate cell growth (Sarbassov et al., 2004 [PubMed 15268862]).[supplied by OMIM, Mar 2008]

RICTOR Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RICTOR	NM_152756.5	c.97+15857C>T		intron_variant	Intron 2 of 37	ENST00000357387.8	NP_689969.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RICTOR	ENST00000357387.8	c.97+15857C>T		intron_variant	Intron 2 of 37	1	NM_152756.5	ENSP00000349959.3

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56648 AN: 151568 Hom.: 10823 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.373 AC: 56653 AN: 151686 Hom.: 10820 Cov.: 32 AF XY: 0.379 AC XY: 28101 AN XY: 74104

African (AFR) AF: 0.294 AC: 12174 AN: 41388

American (AMR) AF: 0.380 AC: 5791 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2458 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4808

European-Finnish (FIN) AF: 0.466 AC: 4900 AN: 10516

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27117 AN: 67812

Other (OTH) AF: 0.353 AC: 741 AN: 2102

Alfa AF: 0.368 Hom.: 7360

Bravo AF: 0.363

Asia WGS AF: 0.350 AC: 1215 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.086
DANN	Benign	0.47
PhyloP100		-1.0
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: rs13160161; hg19: chr5-39058356;