rs9904537

Variant names:

• chr17-32228084-G-A
• rs9904537
• ENST00000583788.1:n.25C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-32228084-G-A
• chr17-32228084-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583788.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBL5P2	ENST00000583788.1	TSL:6	n.25C>T		non_coding_transcript_exon	Exon 1 of 1
	RHOT1	ENST00000580392.5	TSL:3	c.359+19775G>A		intron	N/A	ENSP00000463532.1
	RHOT1	ENST00000584852.1	TSL:5	c.131+16846G>A		intron	N/A	ENSP00000461992.1

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

African (AFR) AF: 0.170 AC: 4583 AN: 27002

American (AMR) AF: 0.238 AC: 10274 AN: 43116

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 4406 AN: 22878

East Asian (EAS) AF: 0.211 AC: 7583 AN: 35906

South Asian (SAS) AF: 0.263 AC: 20987 AN: 79824

European-Finnish (FIN) AF: 0.140 AC: 6931 AN: 49466

Middle Eastern (MID) AF: 0.211 AC: 1048 AN: 4966

European-Non Finnish (NFE) AF: 0.143 AC: 121818 AN: 851974

Other (OTH) AF: 0.167 AC: 8131 AN: 48768

GnomAD4 genome AF: 0.183 AC: 27872 AN: 151978 Hom.: 2657 Cov.: 30 AF XY: 0.183 AC XY: 13578 AN XY: 74284

African (AFR) AF: 0.192 AC: 7951 AN: 41454

American (AMR) AF: 0.186 AC: 2839 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1142 AN: 5132

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4810

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10558

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11889 AN: 67958

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.0850 Hom.: 117

Bravo AF: 0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.80
PhyloP100		0.79
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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