rs15563

Positions:

• chr17-48927831-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_023079.5(UBE2Z):​c.*697A>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 0.412 in 152,490 control chromosomes in the GnomAD database, including 15,508 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 (15428 hom., cov: 31)
  • Exomes 𝑓: 0.57 (80 hom.)
• Consequence: UBE2Z NM_023079.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2Z	NM_023079.5	c.*697A>G		3_prime_UTR_variant	7/7	ENST00000360943.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2Z	ENST00000360943.10	c.*697A>G		3_prime_UTR_variant	7/7	1	NM_023079.5	P1
UBE2Z	ENST00000513342.5	n.3027A>G		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62601 AN: 151894 Hom.: 15434 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.567 AC: 271 AN: 478 Hom.: 80 Cov.: 0 AF XY: 0.561 AC XY: 165 AN XY: 294

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.595

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.412 AC: 62589 AN: 152012 Hom.: 15428 Cov.: 31 AF XY: 0.415 AC XY: 30862 AN XY: 74304

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.441

Alfa AF: 0.520 Hom.: 40405

Bravo AF: 0.393

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs15563; hg19: chr17-47005193;