17-48928147-T-G

Variant names:

• chr17-48928147-T-G
• rs1057897
• NM_023079.5:c.*1013T>G

Variant summary

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

The NM_023079.5(UBE2Z):​c.*1013T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,008 control chromosomes in the GnomAD database, including 15,412 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 0.41 (15401 hom., cov: 31)
  • Exomes 𝑓: 0.53 (11 hom.)
• Consequence: UBE2Z NM_023079.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 26 publications found

Genes affected

UBE2Z (HGNC:25847): (ubiquitin conjugating enzyme E2 Z) This gene encodes an enzyme which ubiquitinates proteins which participate in signaling pathways and apoptosis. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2Z	NM_023079.5	c.*1013T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000360943.10	NP_075567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2Z	ENST00000360943.10	c.*1013T>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_023079.5	ENSP00000354201.5
UBE2Z	ENST00000513342.5	n.3343T>G		non_coding_transcript_exon_variant	Exon 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62527 AN: 151832 Hom.: 15407 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.534 AC: 31 AN: 58 Hom.: 11 Cov.: 0 AF XY: 0.658 AC XY: 25 AN XY: 38

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.604 AC: 29 AN: 48

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.411 AC: 62515 AN: 151950 Hom.: 15401 Cov.: 31 AF XY: 0.415 AC XY: 30807 AN XY: 74236

African (AFR) AF: 0.132 AC: 5466 AN: 41488

American (AMR) AF: 0.412 AC: 6290 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3659 AN: 5156

South Asian (SAS) AF: 0.507 AC: 2437 AN: 4810

European-Finnish (FIN) AF: 0.543 AC: 5715 AN: 10532

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35602 AN: 67930

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.494 Hom.: 21454

Bravo AF: 0.393

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.24
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: rs1057897; hg19: chr17-47005509;