chr7-151481337-T-A

Variant names:

• chr7-151481337-T-A
• rs965118
• NM_005614.4:c.192+3400A>T

Variant summary

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

The NM_005614.4(RHEB):​c.192+3400A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,140 control chromosomes in the GnomAD database, including 14,211 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 0.40 (14211 hom., cov: 32)
• Consequence: RHEB NM_005614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 4 publications found

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]

RHEB Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005614.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHEB	NM_005614.4	MANE Select	c.192+3400A>T		intron	N/A	NP_005605.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHEB	ENST00000262187.10	TSL:1 MANE Select	c.192+3400A>T		intron	N/A	ENSP00000262187.5
	RHEB	ENST00000472642.5	TSL:3	c.-124+3400A>T		intron	N/A	ENSP00000420726.1
	RHEB	ENST00000496004.5	TSL:2	c.-124+3400A>T		intron	N/A	ENSP00000418161.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60610 AN: 152022 Hom.: 14204 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.398 AC: 60620 AN: 152140 Hom.: 14211 Cov.: 32 AF XY: 0.404 AC XY: 30070 AN XY: 74368

African (AFR) AF: 0.137 AC: 5683 AN: 41512

American (AMR) AF: 0.441 AC: 6730 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2123 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2201 AN: 5174

South Asian (SAS) AF: 0.597 AC: 2879 AN: 4820

European-Finnish (FIN) AF: 0.487 AC: 5153 AN: 10574

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34522 AN: 67994

Other (OTH) AF: 0.416 AC: 879 AN: 2112

Alfa AF: 0.438 Hom.: 2026

Bravo AF: 0.378

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.43
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: rs965118; hg19: chr7-151178423;