rs278037

Variant names:

• chr13-29850490-C-T
• rs278037
• NM_007106.4:c.-952G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

UBL3 (HGNC:12504): (ubiquitin like 3) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UBL3	NM_007106.4	c.-952G>A		5_prime_UTR_variant	Exon 1 of 5	ENST00000380680.5	NP_009037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBL3	ENST00000380680.5	c.-952G>A		5_prime_UTR_variant	Exon 1 of 5	1	NM_007106.4	ENSP00000370055.4

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

African (AFR) AF: 0.583 AC: 7 AN: 12

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 2 AN: 6

East Asian (EAS) AF: 0.214 AC: 3 AN: 14

South Asian (SAS) AF: 0.111 AC: 23 AN: 208

European-Finnish (FIN) AF: 0.0556 AC: 1 AN: 18

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.157 AC: 50 AN: 318

Other (OTH) AF: 0.375 AC: 3 AN: 8

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

African (AFR) AF: 0.260 AC: 10800 AN: 41516

American (AMR) AF: 0.165 AC: 2520 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 519 AN: 3472

East Asian (EAS) AF: 0.0708 AC: 365 AN: 5158

South Asian (SAS) AF: 0.169 AC: 816 AN: 4826

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10604

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10745 AN: 67966

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.162 Hom.: 2029

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
PhyloP100		-0.069
PromoterAI		-0.11	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs278037; hg19: chr13-30424627;