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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

Genes affected

RHOU (HGNC:):

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	UniProt
RHOU	NR_037962.1	n.387-10895G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;