rs7302

Variant names:

• chr16-1325262-T-A
• rs7302
• NM_003345.5:c.*469T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-1325262-T-A
• chr16-1325262-T-G

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.*469T>A variant causes a 3 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBE2I NM_003345.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 24 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=-0.65).

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.*469T>A		3_prime_UTR	Exon 7 of 7	NP_003336.1	P63279
	UBE2I	NM_194259.3		c.*469T>A		3_prime_UTR	Exon 8 of 8	NP_919235.1	P63279
	UBE2I	NM_194260.3		c.*469T>A		3_prime_UTR	Exon 7 of 7	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.*469T>A		3_prime_UTR	Exon 7 of 7	ENSP00000380649.3	P63279
	UBE2I	ENST00000567074.7	TSL:1	c.*469T>A		3_prime_UTR	Exon 6 of 6	ENSP00000455893.2	P63279
	UBE2I	ENST00000711312.1		c.*469T>A		3_prime_UTR	Exon 8 of 8	ENSP00000518684.1	A0AAA9YHQ8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 9180 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4918

African (AFR) AF: 0.00 AC: 0 AN: 60

American (AMR) AF: 0.00 AC: 0 AN: 1362

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 78

East Asian (EAS) AF: 0.00 AC: 0 AN: 218

South Asian (SAS) AF: 0.00 AC: 0 AN: 1106

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1654

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 18

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4328

Other (OTH) AF: 0.00 AC: 0 AN: 356

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 96120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.0
DANN	Benign	0.50
PhyloP100		1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7302;

hg19: chr16-1375263;