ENST00000648259.1:n.356+7892T>G

Variant names:

• chr17-22191121-T-G
• rs4889730
• ENST00000648259.1:n.356+7892T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648259.1(UBBP4):​n.356+7892T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,586 control chromosomes in the GnomAD database, including 24,423 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 0.56 (24423 hom., cov: 32)
• Consequence: UBBP4 ENST00000648259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 10 publications found

Genes affected

UBBP4 (HGNC:):

UBBP4 (HGNC:12467): (ubiquitin B pseudogene 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648259.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	NR_176224.1		n.349+7892T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	ENST00000648259.1		n.356+7892T>G		intron	N/A
	UBBP4	ENST00000688301.2		n.245-12966T>G		intron	N/A
	UBBP4	ENST00000765024.1		n.233+7892T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.561 AC: 84962 AN: 151468 Hom.: 24413 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.561 AC: 85009 AN: 151586 Hom.: 24423 Cov.: 32 AF XY: 0.552 AC XY: 40892 AN XY: 74088

African (AFR) AF: 0.497 AC: 20581 AN: 41384

American (AMR) AF: 0.469 AC: 7132 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2532 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5168

South Asian (SAS) AF: 0.523 AC: 2519 AN: 4812

European-Finnish (FIN) AF: 0.540 AC: 5685 AN: 10528

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42874 AN: 67716

Other (OTH) AF: 0.589 AC: 1240 AN: 2104

Alfa AF: 0.609 Hom.: 58320

Bravo AF: 0.554

Asia WGS AF: 0.428 AC: 1485 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		0.073

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4889730; hg19: chr17-21717727;