16-1322182-G-C

Variant names:

• chr16-1322182-G-C
• rs8052688
• NM_003345.5:c.413+1665G>C

Variant summary

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

The NM_003345.5(UBE2I):​c.413+1665G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 150,932 control chromosomes in the GnomAD database, including 4,518 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 0.22 (4518 hom., cov: 29)
• Consequence: UBE2I NM_003345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 10 publications found

Genes affected

UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000261505 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003345.5. 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
	UBE2I	NM_003345.5	MANE Select	c.413+1665G>C		intron	N/A	NP_003336.1	P63279
	UBE2I	NM_194259.3		c.413+1665G>C		intron	N/A	NP_919235.1	P63279
	UBE2I	NM_194260.3		c.413+1665G>C		intron	N/A	NP_919236.1	P63279

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2I	ENST00000397514.8	TSL:1 MANE Select	c.413+1665G>C		intron	N/A	ENSP00000380649.3	P63279
	UBE2I	ENST00000567074.7	TSL:1	c.413+1665G>C		intron	N/A	ENSP00000455893.2	P63279
	UBE2I	ENST00000711312.1		c.569+1665G>C		intron	N/A	ENSP00000518684.1	A0AAA9YHQ8

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33189 AN: 150820 Hom.: 4512 Cov.: 29

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.220 AC: 33227 AN: 150932 Hom.: 4518 Cov.: 29 AF XY: 0.218 AC XY: 16043 AN XY: 73720

African (AFR) AF: 0.378 AC: 15402 AN: 40786

American (AMR) AF: 0.255 AC: 3870 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3468

East Asian (EAS) AF: 0.0436 AC: 226 AN: 5186

South Asian (SAS) AF: 0.148 AC: 711 AN: 4806

European-Finnish (FIN) AF: 0.141 AC: 1461 AN: 10390

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10722 AN: 67848

Other (OTH) AF: 0.203 AC: 422 AN: 2082

Alfa AF: 0.0781 Hom.: 98

Bravo AF: 0.239

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.0
DANN	Benign	0.87
PhyloP100		-0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs8052688; hg19: chr16-1372183;