chr2-169910627-T-C

Variant names:

• chr2-169910627-T-C
• rs10200004
• NM_172070.4:c.1780-3433T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172070.4(UBR3):​c.1780-3433T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,996 control chromosomes in the GnomAD database, including 5,702 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 0.27 (5702 hom., cov: 32)
• Consequence: UBR3 NM_172070.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBR3	NM_172070.4	c.1780-3433T>C		intron_variant	Intron 10 of 38	ENST00000272793.11	NP_742067.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBR3	ENST00000272793.11	c.1780-3433T>C		intron_variant	Intron 10 of 38	5	NM_172070.4	ENSP00000272793.5

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40798 AN: 151878 Hom.: 5695 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.269 AC: 40841 AN: 151996 Hom.: 5702 Cov.: 32 AF XY: 0.272 AC XY: 20234 AN XY: 74304

African (AFR) AF: 0.309 AC: 12813 AN: 41474

American (AMR) AF: 0.221 AC: 3372 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3462

East Asian (EAS) AF: 0.418 AC: 2157 AN: 5164

South Asian (SAS) AF: 0.412 AC: 1983 AN: 4816

European-Finnish (FIN) AF: 0.224 AC: 2366 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16258 AN: 67906

Other (OTH) AF: 0.248 AC: 524 AN: 2114

Alfa AF: 0.266 Hom.: 734

Bravo AF: 0.268

Asia WGS AF: 0.425 AC: 1476 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.18
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: rs10200004; hg19: chr2-170767137;