Variant rs9904537 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000583788.1(UBL5P2):n.25C>T 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 0.162 in 1,315,878 control chromosomes in the GnomAD database, including 18,513 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 0.18 ( 2657 hom., cov: 30)

Exomes 𝑓: 0.16 ( 15856 hom. )

Consequence

UBL5P2
ENST00000583788.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.787

Variant links:

Genes affected

UBL5P2 (HGNC:44640): (ubiquitin like 5 pseudogene 2)

UBL5P2 links:

RHOT1 (HGNC:21168): (ras homolog family member T1) Predicted to enable GTP binding activity and GTPase activity. Involved in cellular homeostasis; mitochondrial outer membrane permeabilization; and mitochondrion transport along microtubule. Is integral component of mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

RHOT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
UBL5P2	ENST00000583788.1 linkuse as main transcript	n.25C>T	non_coding_transcript_exon_variant	1/1
RHOT1	ENST00000580392.5 linkuse as main transcript	c.360+19775G>A	intron_variant		3
RHOT1	ENST00000584852.1 linkuse as main transcript	c.131+16846G>A	intron_variant		5
RHOT1	ENST00000582586.1 linkuse as main transcript	n.59-13711G>A	intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27841

AN:

151860

Hom.:

2650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.160

AC:

185761

AN:

1163900

Hom.:

15856

Cov.:

AF XY:

0.165

AC XY:

97452

AN XY:

591196

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.238

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.263

Gnomad4 FIN exome

AF:

0.140

Gnomad4 NFE exome

AF:

0.143

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.183

AC:

27872

AN:

151978

Hom.:

2657

Cov.:

AF XY:

0.183

AC XY:

13578

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.192

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.223

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.175

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.0802

Hom.:

101

Bravo

AF:

0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.8

DANN

Benign

0.80

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over