dbSNP rs6426514: RHOU:c.*628G>A (chr1-228744368-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021205.6(RHOU):c.*628G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,234 control chromosomes in the GnomAD database, including 780 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 0.097 ( 780 hom., cov: 33)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

RHOU
NM_021205.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.853

Publications

22 publications found

Variant links:

Genes affected

RHOU (HGNC:17794): (ras homolog family member U) This gene encodes a member of the Rho family of GTPases. This protein can activate PAK1 and JNK1, and can induce filopodium formation and stress fiber dissolution. It may also mediate the effects of WNT1 signaling in the regulation of cell morphology, cytoskeletal organization, and cell proliferation. A non-coding transcript variant of this gene results from naturally occurring read-through transcription between this locus and the neighboring DUSP5P (dual specificity phosphatase 5 pseudogene) locus.[provided by RefSeq, Mar 2011]

RHOU 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RHOU	NM_021205.6 link	c.*628G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000366691.4	NP_067028.1	Q7L0Q8-1A0A024R3Q7
RHOU	NR_037962.1 link	n.1529G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RHOU	ENST00000366691.4 link	c.*628G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_021205.6	ENSP00000355652.3		Q7L0Q8-1

Frequencies

GnomAD3 genomes

AF:

0.0969

AC:

14743

AN:

152100

Hom.:

778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.0802

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0319

Gnomad SAS

AF:

0.0294

Gnomad FIN

AF:

0.0548

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.0968

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.143

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0969

AC:

14749

AN:

152218

Hom.:

780

Cov.:

AF XY:

0.0935

AC XY:

6962

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.117

AC:

4847

AN:

41542

American (AMR)

AF:

0.105

AC:

1605

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

421

AN:

3470

East Asian (EAS)

AF:

0.0320

AC:

166

AN:

5184

South Asian (SAS)

AF:

0.0297

AC:

143

AN:

4822

European-Finnish (FIN)

AF:

0.0548

AC:

580

AN:

10586

Middle Eastern (MID)

AF:

0.216

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0968

AC:

6582

AN:

67998

Other (OTH)

AF:

0.127

AC:

269

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

688

1376

2064

2752

3440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0993

Hom.:

2241

Bravo

AF:

0.103

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.9

(source)

DANN

Benign

0.35

PhyloP100

0.85

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over