NM_003345.5:c.151-314G>C

Variant names:

• chr16-1315340-G-C
• rs11248866
• NM_003345.5:c.151-314G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003345.5(UBE2I):​c.151-314G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBE2I NM_003345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 8 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2I	NM_003345.5	c.151-314G>C		intron_variant	Intron 3 of 6	ENST00000397514.8	NP_003336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2I	ENST00000397514.8	c.151-314G>C		intron_variant	Intron 3 of 6	1	NM_003345.5	ENSP00000380649.3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 249336 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 131606

African (AFR) AF: 0.00 AC: 0 AN: 7768

American (AMR) AF: 0.00 AC: 0 AN: 11754

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7148

East Asian (EAS) AF: 0.00 AC: 0 AN: 14714

South Asian (SAS) AF: 0.00 AC: 0 AN: 34102

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12672

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1036

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 146176

Other (OTH) AF: 0.00 AC: 0 AN: 13966

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.20
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11248866; hg19: chr16-1365341;