chr7-151469166-A-C

Position:

• chr7-151469166-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005614.4(RHEB):​c.462+1405T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,920 control chromosomes in the GnomAD database, including 5,662 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 0.24 (5662 hom., cov: 32)
• Consequence: RHEB NM_005614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

Genes affected

RHEB (HGNC:10011): (Ras homolog, mTORC1 binding) This gene is a member of the small GTPase superfamily and encodes a lipid-anchored, cell membrane protein with five repeats of the RAS-related GTP-binding region. This protein is vital in regulation of growth and cell cycle progression due to its role in the insulin/TOR/S6K signaling pathway. The protein has GTPase activity and shuttles between a GDP-bound form and a GTP-bound form, and farnesylation of the protein is required for this activity. Three pseudogenes have been mapped, two on chromosome 10 and one on chromosome 22. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHEB	NM_005614.4	c.462+1405T>G		intron_variant		ENST00000262187.10	NP_005605.1
RHEB	XM_011516457.3	c.429+1405T>G		intron_variant			XP_011514759.1
RHEB	XM_024446854.2	c.429+1405T>G		intron_variant			XP_024302622.1
RHEB	XM_047420685.1	c.429+1405T>G		intron_variant			XP_047276641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RHEB	ENST00000262187.10	c.462+1405T>G		intron_variant		1	NM_005614.4	ENSP00000262187	P1
RHEB	ENST00000472642.5	c.147+1405T>G		intron_variant		3		ENSP00000420726
RHEB	ENST00000496004.5	c.147+1405T>G		intron_variant		2		ENSP00000418161
RHEB	ENST00000478470.5	c.*410+1405T>G		intron_variant, NMD_transcript_variant		5		ENSP00000417802

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36789 AN: 151804 Hom.: 5653 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.242 AC: 36795 AN: 151920 Hom.: 5662 Cov.: 32 AF XY: 0.251 AC XY: 18614 AN XY: 74258

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.253

Alfa AF: 0.271 Hom.: 3448

Bravo AF: 0.229

Asia WGS AF: 0.410 AC: 1423 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.49

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: rs717775; hg19: chr7-151166252;