rs719199

Positions:

• chr13-29815115-C-G
• chr13-29815115-C-T

Variant summary

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

The NM_007106.4(UBL3):​c.27+34397G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,078 control chromosomes in the GnomAD database, including 1,290 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 0.11 (1290 hom., cov: 32)
• Consequence: UBL3 NM_007106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBL3	NM_007106.4	c.27+34397G>C		intron_variant		ENST00000380680.5	NP_009037.1
UBL3	XM_047430394.1	c.-121-18204G>C		intron_variant			XP_047286350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBL3	ENST00000380680.5	c.27+34397G>C		intron_variant		1	NM_007106.4	ENSP00000370055	P1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17151 AN: 151960 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.113 AC: 17203 AN: 152078 Hom.: 1290 Cov.: 32 AF XY: 0.116 AC XY: 8659 AN XY: 74348

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0901

Alfa AF: 0.0453 Hom.: 29

Bravo AF: 0.113

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.87
DANN	Benign	0.68

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: rs719199; hg19: chr13-30389252;