rs9904537

chr17-32228084-G-Achr17-32228084-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

Genes affected

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

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]

ACMG classification

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	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBL5P2	ENST00000583788.1	n.25C>T		non_coding_transcript_exon_variant	1/1
RHOT1	ENST00000580392.5	c.360+19775G>A		intron_variant		3
RHOT1	ENST00000584852.1	c.131+16846G>A		intron_variant		5
RHOT1	ENST00000582586.1	n.59-13711G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27841 AN: 151860 Hom.: 2650 Cov.: 30

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.: 20 AF XY: 0.165 AC XY: 97452 AN XY: 591196

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.: 30 AF XY: 0.183 AC XY: 13578 AN XY: 74284

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

Other links and lift over

dbSNP: rs9904537; hg19: chr17-30555103; COSMIC: COSV61715973;