rs2528381

Positions:

• chr7-43927243-A-G
• chr7-43927243-A-T

Variant summary

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

The NM_015983.4(UBE2D4):​c.24+687A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 151,408 control chromosomes in the GnomAD database, including 276 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 0.056 (276 hom., cov: 32)
• Consequence: UBE2D4 NM_015983.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

UBE2D4 (HGNC:21647): (ubiquitin conjugating enzyme E2 D4 (putative)) Enables ubiquitin conjugating enzyme activity. Involved in protein polyubiquitination. Acts upstream of or within protein ubiquitination. Predicted to be part of ubiquitin ligase complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

UBE2D4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2D4	NM_015983.4	c.24+687A>G		intron_variant		ENST00000222402.8	NP_057067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2D4	ENST00000222402.8	c.24+687A>G		intron_variant		1	NM_015983.4	ENSP00000222402.2

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8437 AN: 151332 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0119

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0595

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

GnomAD4 genome AF: 0.0558 AC: 8448 AN: 151408 Hom.: 276 Cov.: 32 AF XY: 0.0551 AC XY: 4071 AN XY: 73940

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0119

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.0599

Alfa AF: 0.0428 Hom.: 76

Bravo AF: 0.0582

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.86

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: rs2528381; hg19: chr7-43966842;