ENST00000648259.1:n.167-1085A>G

Variant names:

• chr17-22180454-A-G
• rs1975974
• ENST00000648259.1:n.167-1085A>G

Variant summary

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

The ENST00000648259.1(UBBP4):​n.167-1085A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,096 control chromosomes in the GnomAD database, including 2,805 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 0.18 (2805 hom., cov: 32)
• Consequence: UBBP4 ENST00000648259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 24 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	NR_176224.1		n.160-1085A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	ENST00000648259.1		n.167-1085A>G		intron	N/A
	UBBP4	ENST00000688301.2		n.245-23633A>G		intron	N/A
	UBBP4	ENST00000765024.1		n.44-1085A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27474 AN: 151976 Hom.: 2797 Cov.: 32

Gnomad AFR AF: 0.0951

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.181 AC: 27495 AN: 152096 Hom.: 2805 Cov.: 32 AF XY: 0.180 AC XY: 13400 AN XY: 74366

African (AFR) AF: 0.0952 AC: 3951 AN: 41508

American (AMR) AF: 0.160 AC: 2436 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3468

East Asian (EAS) AF: 0.141 AC: 729 AN: 5172

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2176 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14844 AN: 67988

Other (OTH) AF: 0.214 AC: 453 AN: 2112

Alfa AF: 0.192 Hom.: 4569

Bravo AF: 0.171

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1975974; hg19: chr17-21707060;