ENST00000852849.1:c.-259-2719T>C

Variant names:

• chr16-1299208-T-C
• rs7187167
• ENST00000852849.1:c.-259-2719T>C

Variant summary

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

The ENST00000852849.1(UBE2I):​c.-259-2719T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,016 control chromosomes in the GnomAD database, including 36,730 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 0.69 (36709 hom., cov: 32)
  • Exomes 𝑓: 0.76 (21 hom.)
• Consequence: UBE2I ENST00000852849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 26 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]

UBE2I-AS1 (HGNC:58131):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000852849.1. 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-AS1	NR_198995.1		n.398A>G		non_coding_transcript_exon	Exon 1 of 3
	UBE2I-AS1	NR_198996.1		n.398A>G		non_coding_transcript_exon	Exon 1 of 2
	UBE2I-AS1	NR_198997.1		n.398A>G		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2I	ENST00000852849.1		c.-259-2719T>C		intron	N/A	ENSP00000522908.1
	UBE2I-AS1	ENST00000561649.4	TSL:3	n.428A>G		non_coding_transcript_exon	Exon 1 of 3
	UBE2I-AS1	ENST00000686290.3		n.362A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104917 AN: 151826 Hom.: 36697 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.764 AC: 55 AN: 72 Hom.: 21 Cov.: 0 AF XY: 0.725 AC XY: 29 AN XY: 40

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 10 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.696 AC: 32 AN: 46

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.691 AC: 104976 AN: 151944 Hom.: 36709 Cov.: 32 AF XY: 0.695 AC XY: 51634 AN XY: 74266

African (AFR) AF: 0.599 AC: 24776 AN: 41374

American (AMR) AF: 0.647 AC: 9871 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2505 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4712 AN: 5172

South Asian (SAS) AF: 0.776 AC: 3738 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8128 AN: 10564

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48950 AN: 67976

Other (OTH) AF: 0.674 AC: 1419 AN: 2106

Alfa AF: 0.711 Hom.: 106691

Bravo AF: 0.675

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.35
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7187167; hg19: chr16-1349209;