17-48911235-C-T

Position:

• chr17-48911235-C-T

Variant summary

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

The NM_023079.5(UBE2Z):​c.390+355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 224,654 control chromosomes in the GnomAD database, including 25,066 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 (15404 hom., cov: 32)
  • Exomes 𝑓: 0.50 (9662 hom.)
• Consequence: UBE2Z NM_023079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

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]

UBE2Z (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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/exons	MANE	Protein	UniProt
UBE2Z	NM_023079.5	c.390+355C>T		intron_variant		ENST00000360943.10	NP_075567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2Z	ENST00000360943.10	c.390+355C>T		intron_variant		1	NM_023079.5	ENSP00000354201.5

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62570 AN: 151834 Hom.: 15410 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.498 AC: 36210 AN: 72702 Hom.: 9662 Cov.: 0 AF XY: 0.502 AC XY: 19209 AN XY: 38294

Gnomad4 AFR exome AF: 0.113

Gnomad4 AMR exome AF: 0.429

Gnomad4 ASJ exome AF: 0.507

Gnomad4 EAS exome AF: 0.706

Gnomad4 SAS exome AF: 0.465

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.496

GnomAD4 genome AF: 0.412 AC: 62559 AN: 151952 Hom.: 15404 Cov.: 32 AF XY: 0.415 AC XY: 30836 AN XY: 74274

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.441

Alfa AF: 0.525 Hom.: 27744

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	-0.83
CADD	Benign	2.4
DANN	Benign	0.74

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: rs46522; hg19: chr17-46988597;