rs278037

Positions:

• chr13-29850490-C-T

Variant summary

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

The NM_007106.4(UBL3):​c.-952G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,742 control chromosomes in the GnomAD database, including 2,773 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 (2762 hom., cov: 32)
  • Exomes 𝑓: 0.15 (11 hom.)
• Consequence: UBL3 NM_007106.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

UBL3 (HGNC:12504): (ubiquitin like 3) Located in extracellular exosome. [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 (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBL3	NM_007106.4	c.-952G>A		5_prime_UTR_variant	1/5	ENST00000380680.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBL3	ENST00000380680.5	c.-952G>A		5_prime_UTR_variant	1/5	1	NM_007106.4	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27694 AN: 152034 Hom.: 2759 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0706

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.153 AC: 90 AN: 590 Hom.: 11 Cov.: 0 AF XY: 0.135 AC XY: 52 AN XY: 384

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0556

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.182 AC: 27712 AN: 152152 Hom.: 2762 Cov.: 32 AF XY: 0.178 AC XY: 13257 AN XY: 74392

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.181

Alfa AF: 0.164 Hom.: 1287

Bravo AF: 0.187

Asia WGS AF: 0.111 AC: 388 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	16
DANN	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs278037; hg19: chr13-30424627;