rs9294266

chr6-82900346-T-G

Variant summary

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

The NM_198920.3(UBE3D):c.1150-7304A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 152,220 control chromosomes in the GnomAD database, including 677 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 0.082 (677 hom., cov: 33)
• Consequence: UBE3D NM_198920.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

Genes affected

UBE3D (HGNC:21381): (ubiquitin protein ligase E3D) Enables cyclin binding activity; ubiquitin protein ligase activity; and ubiquitin-like protein conjugating enzyme binding activity. Involved in protein autoubiquitination; protein monoubiquitination; and protein polyubiquitination. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE3D	NM_198920.3	c.1150-7304A>C		intron_variant		ENST00000369747.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE3D	ENST00000369747.8	c.1150-7304A>C		intron_variant		1	NM_198920.3	P1
UBE3D	ENST00000237186.10	c.*1001-7304A>C		intron_variant, NMD_transcript_variant		1
UBE3D	ENST00000509102.5	c.*269-7304A>C		intron_variant, NMD_transcript_variant		1
UBE3D	ENST00000430071.6	c.*845-7304A>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12512 AN: 152102 Hom.: 677 Cov.: 33

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.106

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0822 AC: 12518 AN: 152220 Hom.: 677 Cov.: 33 AF XY: 0.0830 AC XY: 6179 AN XY: 74422

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.0804

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0978

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0919 Hom.: 388

Bravo AF: 0.0868

Asia WGS AF: 0.0760 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.7
Dann	Benign	0.76

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: rs9294266; hg19: chr6-83610065;