chr6-82900346-T-G

Variant names:

• chr6-82900346-T-G
• rs9294266
• NM_198920.3:c.1150-7304A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198920.3. 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
	UBE3D	NM_198920.3	MANE Select	c.1150-7304A>C		intron	N/A	NP_944602.1	Q7Z6J8
	UBE3D	NM_001304437.2		c.1054-7304A>C		intron	N/A	NP_001291366.1
	UBE3D	NM_001350602.2		c.1054-7304A>C		intron	N/A	NP_001337531.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE3D	ENST00000369747.8	TSL:1 MANE Select	c.1150-7304A>C		intron	N/A	ENSP00000358762.3	Q7Z6J8
	UBE3D	ENST00000237186.10	TSL:1	n.*1001-7304A>C		intron	N/A	ENSP00000237186.6	J3KMY4
	UBE3D	ENST00000509102.5	TSL:1	n.*269-7304A>C		intron	N/A	ENSP00000427101.1	D6RD24

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

African (AFR) AF: 0.0200 AC: 830 AN: 41570

American (AMR) AF: 0.165 AC: 2514 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.0574 AC: 297 AN: 5176

South Asian (SAS) AF: 0.0804 AC: 387 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1180 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0978 AC: 6650 AN: 68000

Other (OTH) AF: 0.107 AC: 226 AN: 2116

Alfa AF: 0.0849 Hom.: 518

Bravo AF: 0.0868

Asia WGS AF: 0.0760 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		0.42
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: rs9294266; hg19: chr6-83610065;