Variant 10-16816994-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012425.4(RSU1):c.88A>G(p.Met30Val) variant causes a missense change. The variant allele was found at a frequency of 0.00828 in 1,613,768 control chromosomes in the GnomAD database, including 752 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0096 ( 66 hom., cov: 33)

Exomes 𝑓: 0.0081 ( 686 hom. )

Consequence

RSU1
NM_012425.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.05

Variant links:

Genes affected

RSU1 (HGNC:10464): (Ras suppressor protein 1) This gene encodes a protein that is involved in the Ras signal transduction pathway, growth inhibition, and nerve-growth factor induced differentiation processes, as determined in mouse and human cell line studies. In mouse, the encoded protein was initially isolated based on its ability to inhibit v-Ras transformation. Multiple alternatively spliced transcript variants for this gene have been reported; one of these variants was found only in glioma tumors. [provided by RefSeq, Jul 2008]

RSU1 links:

RSU1 (HGNC:):

RSU1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017714202).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSU1	NM_012425.4 linkuse as main transcript	c.88A>G	p.Met30Val	missense_variant	2/9	ENST00000345264.10	NP_036557.1	Q15404-1
RSU1	XM_047425617.1 linkuse as main transcript	c.88A>G	p.Met30Val	missense_variant	1/7		XP_047281573.1
RSU1	NM_152724.3 linkuse as main transcript	c.-51+321A>G		intron_variant			NP_689937.2	Q15404-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10 linkuse as main transcript	c.88A>G	p.Met30Val	missense_variant	2/9	1	NM_012425.4	ENSP00000339521.5		Q15404-1

Frequencies

GnomAD3 genomes

AF:

0.00962

AC:

1465

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00223

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.0279

Gnomad FIN

AF:

0.0409

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00126

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.0171

AC:

4294

AN:

251442

Hom.:

205

AF XY:

0.0172

AC XY:

2338

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.000376

Gnomad ASJ exome

AF:

0.00367

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.0246

Gnomad FIN exome

AF:

0.0413

Gnomad NFE exome

AF:

0.00154

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.00814

AC:

11896

AN:

1461426

Hom.:

686

Cov.:

AF XY:

0.00860

AC XY:

6255

AN XY:

727046

show subpopulations

Gnomad4 AFR exome

AF:

0.000179

Gnomad4 AMR exome

AF:

0.000559

Gnomad4 ASJ exome

AF:

0.00341

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.0241

Gnomad4 FIN exome

AF:

0.0387

Gnomad4 NFE exome

AF:

0.000507

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.00960

AC:

1462

AN:

152342

Hom.:

Cov.:

AF XY:

0.0125

AC XY:

928

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.000216

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.0279

Gnomad4 FIN

AF:

0.0409

Gnomad4 NFE

AF:

0.00126

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00626

Hom.:

Bravo

AF:

0.00697

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.0169

AC:

2049

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

EpiCase

AF:

0.000872

EpiControl

AF:

0.000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.018

T;T

Eigen

Benign

-0.11

Eigen_PC

Benign

0.042

FATHMM_MKL

Benign

0.71

LIST_S2

Uncertain

0.90

.;D

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

L;L

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.59

N;N

REVEL

Benign

0.080

Sift

Benign

0.24

T;T

Sift4G

Benign

0.16

T;T

Polyphen

0.0010

B;B

Vest4

0.33

MPC

0.30

ClinPred

0.028

GERP RS

4.1

Varity_R

0.22

gMVP

0.41

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over