Variant rs1049632 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_012425.4(RSU1):c.351G>T(p.Thr117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,610,744 control chromosomes in the GnomAD database, including 68,063 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 0.38 ( 13426 hom., cov: 31)

Exomes 𝑓: 0.26 ( 54637 hom. )

Consequence

RSU1
NM_012425.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.708

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP7

Synonymous conserved (PhyloP=0.708 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RSU1	NM_012425.4 linkuse as main transcript	c.351G>T	p.Thr117=	synonymous_variant	5/9	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3 linkuse as main transcript	c.192G>T	p.Thr64=	synonymous_variant	4/8		NP_689937.2
RSU1	XM_047425617.1 linkuse as main transcript	c.351G>T	p.Thr117=	synonymous_variant	4/7		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10 linkuse as main transcript	c.351G>T	p.Thr117=	synonymous_variant	5/9	1	NM_012425.4	ENSP00000339521	P1	Q15404-1

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57219

AN:

151770

Hom.:

13372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.373

GnomAD3 exomes

AF:

0.284

AC:

71073

AN:

249912

Hom.:

11866

AF XY:

0.276

AC XY:

37230

AN XY:

135096

show subpopulations

Gnomad AFR exome

AF:

0.676

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.251

Gnomad EAS exome

AF:

0.416

Gnomad SAS exome

AF:

0.225

Gnomad FIN exome

AF:

0.224

Gnomad NFE exome

AF:

0.257

Gnomad OTH exome

AF:

0.285

GnomAD4 exome

AF:

0.262

AC:

382789

AN:

1458854

Hom.:

54637

Cov.:

AF XY:

0.260

AC XY:

188365

AN XY:

725738

show subpopulations

Gnomad4 AFR exome

AF:

0.684

Gnomad4 AMR exome

AF:

0.235

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.379

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.286

GnomAD4 genome

AF:

0.378

AC:

57341

AN:

151890

Hom.:

13426

Cov.:

AF XY:

0.372

AC XY:

27639

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.671

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.226

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.288

Hom.:

3941

Bravo

AF:

0.400

Asia WGS

AF:

0.361

AC:

1254

AN:

3478

EpiCase

AF:

0.257

EpiControl

AF:

0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

4.3

DANN

Benign

0.57

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