rs7225527

chr17-32227931-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000583788.1(UBL5P2):n.178T>C 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 0.18 in 963,584 control chromosomes in the GnomAD database, including 16,887 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 (2578 hom., cov: 29)
  • Exomes 𝑓: 0.18 (14309 hom.)
• Consequence: UBL5P2 ENST00000583788.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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.178T>C		non_coding_transcript_exon_variant	1/1
RHOT1	ENST00000580392.5	c.360+19622A>G		intron_variant		3
RHOT1	ENST00000584852.1	c.131+16693A>G		intron_variant		5
RHOT1	ENST00000582586.1	n.59-13864A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27441 AN: 151632 Hom.: 2571 Cov.: 29

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.180 AC: 146036 AN: 811834 Hom.: 14309 Cov.: 11 AF XY: 0.184 AC XY: 79068 AN XY: 428730

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.279

Gnomad4 FIN exome AF: 0.142

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.181 AC: 27471 AN: 151750 Hom.: 2578 Cov.: 29 AF XY: 0.181 AC XY: 13382 AN XY: 74136

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.183

Alfa AF: 0.179 Hom.: 305

Bravo AF: 0.184

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	2.3
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7225527; hg19: chr17-30554950; COSMIC: COSV61715972;