Genetic Variant RSU1:c.161-36T>G (chr10-16764546-A-C) – 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.161-36T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,594,874 control chromosomes in the GnomAD database, including 25,700 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 0.20 ( 3460 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22240 hom. )

Consequence

RSU1
NM_012425.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166

Publications

5 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4 link	c.161-36T>G	intron_variant	Intron 3 of 8	ENST00000345264.10	NP_036557.1	Q15404-1
RSU1	NM_152724.3 link	c.2-36T>G	intron_variant	Intron 2 of 7		NP_689937.2	Q15404-2
RSU1	XM_047425617.1 link	c.161-36T>G	intron_variant	Intron 2 of 6		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10 link	c.161-36T>G		intron_variant	Intron 3 of 8	1	NM_012425.4	ENSP00000339521.5		Q15404-1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30540

AN:

152076

Hom.:

3456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.0183

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.222

GnomAD2 exomes

AF:

0.155

AC:

37305

AN:

241292

AF XY:

0.153

show subpopulations

Gnomad AFR exome

AF:

0.298

Gnomad AMR exome

AF:

0.113

Gnomad ASJ exome

AF:

0.198

Gnomad EAS exome

AF:

0.0180

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.182

Gnomad OTH exome

AF:

0.186

GnomAD4 exome

AF:

0.169

AC:

243653

AN:

1442680

Hom.:

22240

Cov.:

AF XY:

0.166

AC XY:

119152

AN XY:

716138

show subpopulations

African (AFR)

AF:

0.299

AC:

9830

AN:

32832

American (AMR)

AF:

0.121

AC:

5212

AN:

42922

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

4854

AN:

25718

East Asian (EAS)

AF:

0.0225

AC:

880

AN:

39132

South Asian (SAS)

AF:

0.102

AC:

8536

AN:

83584

European-Finnish (FIN)

AF:

0.129

AC:

6851

AN:

53124

Middle Eastern (MID)

AF:

0.194

AC:

1106

AN:

5692

European-Non Finnish (NFE)

AF:

0.178

AC:

195989

AN:

1100022

Other (OTH)

AF:

0.174

AC:

10395

AN:

59654

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

8317

16634

24952

33269

41586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.201

AC:

30564

AN:

152194

Hom.:

3460

Cov.:

AF XY:

0.196

AC XY:

14580

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.294

AC:

12208

AN:

41484

American (AMR)

AF:

0.184

AC:

2812

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

668

AN:

3470

East Asian (EAS)

AF:

0.0183

AC:

AN:

5192

South Asian (SAS)

AF:

0.111

AC:

537

AN:

4832

European-Finnish (FIN)

AF:

0.132

AC:

1399

AN:

10606

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.179

AC:

12188

AN:

68016

Other (OTH)

AF:

0.223

AC:

471

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1253

2506

3758

5011

6264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.184

Hom.:

593

Bravo

AF:

0.211

Asia WGS

AF:

0.0760

AC:

262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.25

(source)

DANN

Benign

0.39

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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10-16764546-A-C

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