rs10489542

Variant names:

• chr1-228726778-G-A
• rs10489542
• NR_037962.1:n.387-10895G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_037962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHOU	NR_037962.1		n.387-10895G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.312 AC: 12925 AN: 41476

American (AMR) AF: 0.176 AC: 2694 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1251 AN: 5174

South Asian (SAS) AF: 0.119 AC: 575 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1546 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0856 AC: 5818 AN: 68004

Other (OTH) AF: 0.155 AC: 328 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10489542; hg19: chr1-228862525;