rs13160161

Positions:

• chr5-39058254-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RICTOR	NM_152756.5	c.97+15857C>T		intron_variant		ENST00000357387.8	NP_689969.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RICTOR	ENST00000357387.8	c.97+15857C>T		intron_variant		1	NM_152756.5	ENSP00000349959	P4

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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.353

Alfa AF: 0.385 Hom.: 3003

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

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: rs13160161; hg19: chr5-39058356;