rs2892463

Positions:

• chr13-29773698-G-T

Variant summary

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

The NM_007106.4(UBL3):​c.137-1500C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,752 control chromosomes in the GnomAD database, including 23,546 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 0.55 (23546 hom., cov: 30)
• Consequence: UBL3 NM_007106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBL3	NM_007106.4	c.137-1500C>A		intron_variant		ENST00000380680.5
UBL3	XM_047430394.1	c.113-1500C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBL3	ENST00000380680.5	c.137-1500C>A		intron_variant		1	NM_007106.4	P1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84059 AN: 151634 Hom.: 23546 Cov.: 30

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.554 AC: 84093 AN: 151752 Hom.: 23546 Cov.: 30 AF XY: 0.553 AC XY: 41030 AN XY: 74172

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.571

Alfa AF: 0.586 Hom.: 51706

Bravo AF: 0.541

Asia WGS AF: 0.472 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.60

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: rs2892463; hg19: chr13-30347835;