rs10489542

Positions:

• chr1-228726778-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_037962.1(RHOU):​n.387-10895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,116 control chromosomes in the GnomAD database, including 2,813 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 0.17 (2813 hom., cov: 32)
• Consequence: RHOU NR_037962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHOU	NR_037962.1	n.387-10895G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25530 AN: 152002 Hom.: 2809 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.157

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.168 AC: 25560 AN: 152116 Hom.: 2813 Cov.: 32 AF XY: 0.172 AC XY: 12770 AN XY: 74370

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.155

Alfa AF: 0.146 Hom.: 446

Bravo AF: 0.179

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489542; hg19: chr1-228862525;