rs2892463

Variant names:

• chr13-29773698-G-T
• rs2892463
• NM_007106.4:c.137-1500C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007106.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBL3	NM_007106.4	MANE Select	c.137-1500C>A		intron	N/A	NP_009037.1	O95164

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBL3	ENST00000380680.5	TSL:1 MANE Select	c.137-1500C>A		intron	N/A	ENSP00000370055.4	O95164

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

African (AFR) AF: 0.500 AC: 20678 AN: 41372

American (AMR) AF: 0.533 AC: 8119 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2126 AN: 3464

East Asian (EAS) AF: 0.392 AC: 2019 AN: 5152

South Asian (SAS) AF: 0.583 AC: 2804 AN: 4812

European-Finnish (FIN) AF: 0.601 AC: 6315 AN: 10516

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40401 AN: 67896

Other (OTH) AF: 0.571 AC: 1205 AN: 2110

Alfa AF: 0.580 Hom.: 76693

Bravo AF: 0.541

Asia WGS AF: 0.472 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		0.41
Mutation Taster		=100/0	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: rs2892463; hg19: chr13-30347835;