2-170077265-G-T

Position:

• chr2-170077265-G-T

Variant summary

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

The NM_172070.4(UBR3):​c.5200-2549G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 740,068 control chromosomes in the GnomAD database, including 684 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 0.051 (381 hom., cov: 32)
  • Exomes 𝑓: 0.022 (303 hom.)
• Consequence: UBR3 NM_172070.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460

Genes affected

UBR3 (HGNC:30467): (ubiquitin protein ligase E3 component n-recognin 3) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including cellular protein metabolic process; sensory perception of smell; and suckling behavior. Predicted to act upstream of or within in utero embryonic development and olfactory behavior. Predicted to be integral component of membrane. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

UBR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBR3	NM_172070.4	c.5200-2549G>T		intron_variant		ENST00000272793.11	NP_742067.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBR3	ENST00000272793.11	c.5200-2549G>T		intron_variant		5	NM_172070.4	ENSP00000272793.5

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7728 AN: 152094 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0397

GnomAD4 exome AF: 0.0216 AC: 12708 AN: 587856 Hom.: 303 Cov.: 4 AF XY: 0.0201 AC XY: 6468 AN XY: 322230

Gnomad4 AFR exome AF: 0.123

Gnomad4 AMR exome AF: 0.0488

Gnomad4 ASJ exome AF: 0.00542

Gnomad4 EAS exome AF: 0.0182

Gnomad4 SAS exome AF: 0.0161

Gnomad4 FIN exome AF: 0.0183

Gnomad4 NFE exome AF: 0.0157

Gnomad4 OTH exome AF: 0.0249

GnomAD4 genome AF: 0.0508 AC: 7734 AN: 152212 Hom.: 381 Cov.: 32 AF XY: 0.0492 AC XY: 3658 AN XY: 74418

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0374 Hom.: 25

Bravo AF: 0.0571

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	4.2
DANN	Benign	0.65

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: rs10497353; hg19: chr2-170933775;