7-151487899-C-T

Variant summary

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

The NM_005614.4(RHEB):c.124+3044G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,006 control chromosomes in the GnomAD database, including 25,104 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 0.57 (25104 hom., cov: 32)
• Consequence: RHEB NM_005614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHEB	NM_005614.4	c.124+3044G>A		intron_variant		ENST00000262187.10
RHEB	XM_011516457.3	c.91+3044G>A		intron_variant
RHEB	XM_024446854.2	c.91+3044G>A		intron_variant
RHEB	XM_047420685.1	c.91+3044G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHEB	ENST00000262187.10	c.124+3044G>A		intron_variant		1	NM_005614.4	P1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86874 AN: 151888 Hom.: 25065 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.572 AC: 86966 AN: 152006 Hom.: 25104 Cov.: 32 AF XY: 0.576 AC XY: 42780 AN XY: 74280

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.570

Alfa AF: 0.559 Hom.: 50524

Bravo AF: 0.576

Asia WGS AF: 0.598 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.76

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: rs3753151; hg19: chr7-151184985;