Genetic Variant RSU1:n.128G>C (chr10-16817336-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000377911.1(RSU1):n.128G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 461,128 control chromosomes in the GnomAD database, including 14,084 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 0.28 ( 8654 hom., cov: 34)

Exomes 𝑓: 0.17 ( 5430 hom. )

Consequence

RSU1
ENST00000377911.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.330

Publications

7 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=-0.58).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4 link	c.-25G>C		5_prime_UTR_variant	Exon 1 of 9	ENST00000345264.10	NP_036557.1	Q15404-1
RSU1	NM_152724.3 link	c.-72G>C		5_prime_UTR_variant	Exon 1 of 8		NP_689937.2	Q15404-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10 link	c.-25G>C		5_prime_UTR_variant	Exon 1 of 9	1	NM_012425.4	ENSP00000339521.5		Q15404-1

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41878

AN:

152134

Hom.:

8637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.0416

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.0906

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.258

GnomAD4 exome

AF:

0.167

AC:

51428

AN:

308876

Hom.:

5430

Cov.:

AF XY:

0.163

AC XY:

26481

AN XY:

162020

show subpopulations

African (AFR)

AF:

0.585

AC:

5291

AN:

9052

American (AMR)

AF:

0.155

AC:

1812

AN:

11708

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

1935

AN:

9862

East Asian (EAS)

AF:

0.0251

AC:

503

AN:

20060

South Asian (SAS)

AF:

0.140

AC:

4470

AN:

31930

European-Finnish (FIN)

AF:

0.0931

AC:

1887

AN:

20278

Middle Eastern (MID)

AF:

0.175

AC:

239

AN:

1368

European-Non Finnish (NFE)

AF:

0.171

AC:

31774

AN:

186016

Other (OTH)

AF:

0.189

AC:

3517

AN:

18602

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1867

3735

5602

7470

9337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.275

AC:

41941

AN:

152252

Hom.:

8654

Cov.:

AF XY:

0.265

AC XY:

19722

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.587

AC:

24378

AN:

41516

American (AMR)

AF:

0.180

AC:

2760

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

649

AN:

3472

East Asian (EAS)

AF:

0.0419

AC:

217

AN:

5182

South Asian (SAS)

AF:

0.145

AC:

703

AN:

4832

European-Finnish (FIN)

AF:

0.0906

AC:

962

AN:

10616

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.170

AC:

11574

AN:

68004

Other (OTH)

AF:

0.255

AC:

540

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1328

2657

3985

5314

6642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0764

Hom.:

Bravo

AF:

0.299

Asia WGS

AF:

0.114

AC:

401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

8.5

(source)

DANN

Benign

0.45

PhyloP100

0.33

PromoterAI

-0.11

Neutral

(source)

Mutation Taster

=300/0

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

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

10-16817336-C-G

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