Genetic Variant RSU1:c.282-45T>C (chr10-16755034-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012425.4(RSU1):c.282-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,169,496 control chromosomes in the GnomAD database, including 58,928 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 0.42 ( 17639 hom., cov: 32)

Exomes 𝑓: 0.27 ( 41289 hom. )

Consequence

RSU1
NM_012425.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851

Publications

6 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4 link	c.282-45T>C	intron_variant	Intron 4 of 8	ENST00000345264.10	NP_036557.1	Q15404-1
RSU1	NM_152724.3 link	c.123-45T>C	intron_variant	Intron 3 of 7		NP_689937.2	Q15404-2
RSU1	XM_047425617.1 link	c.282-45T>C	intron_variant	Intron 3 of 6		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10 link	c.282-45T>C		intron_variant	Intron 4 of 8	1	NM_012425.4	ENSP00000339521.5		Q15404-1

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

63443

AN:

152018

Hom.:

17571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.799

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.405

GnomAD2 exomes

AF:

0.298

AC:

69838

AN:

234722

AF XY:

0.287

show subpopulations

Gnomad AFR exome

AF:

0.807

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.248

Gnomad EAS exome

AF:

0.415

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.293

GnomAD4 exome

AF:

0.267

AC:

271354

AN:

1017360

Hom.:

41289

Cov.:

AF XY:

0.264

AC XY:

138644

AN XY:

524410

show subpopulations

African (AFR)

AF:

0.816

AC:

19361

AN:

23720

American (AMR)

AF:

0.243

AC:

9807

AN:

40436

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

5591

AN:

22330

East Asian (EAS)

AF:

0.379

AC:

14086

AN:

37134

South Asian (SAS)

AF:

0.254

AC:

18824

AN:

74232

European-Finnish (FIN)

AF:

0.224

AC:

11804

AN:

52668

Middle Eastern (MID)

AF:

0.336

AC:

1118

AN:

3326

European-Non Finnish (NFE)

AF:

0.247

AC:

177382

AN:

718304

Other (OTH)

AF:

0.296

AC:

13381

AN:

45210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

8645

17290

25935

34580

43225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4936

9872

14808

19744

24680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.418

AC:

63579

AN:

152136

Hom.:

17639

Cov.:

AF XY:

0.412

AC XY:

30661

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.800

AC:

33202

AN:

41502

American (AMR)

AF:

0.349

AC:

5332

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

914

AN:

3468

East Asian (EAS)

AF:

0.397

AC:

2049

AN:

5156

South Asian (SAS)

AF:

0.259

AC:

1248

AN:

4824

European-Finnish (FIN)

AF:

0.227

AC:

2399

AN:

10586

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17218

AN:

68006

Other (OTH)

AF:

0.410

AC:

867

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1468

2935

4403

5870

7338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.320

Hom.:

2255

Bravo

AF:

0.445

Asia WGS

AF:

0.387

AC:

1345

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.048

(source)

DANN

Benign

0.29

PhyloP100

-0.85

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over