17-22190937-G-A

Variant names:

• chr17-22190937-G-A
• rs17052344
• ENST00000648259.1:n.356+7708G>A

Variant summary

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

The NR_176224.1(UBBP4):​n.349+7708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,668 control chromosomes in the GnomAD database, including 3,058 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 0.20 (3058 hom., cov: 32)
• Consequence: UBBP4 NR_176224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 5 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_176224.1. 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.349+7708G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	ENST00000648259.1		n.356+7708G>A		intron	N/A
	UBBP4	ENST00000688301.2		n.245-13150G>A		intron	N/A
	UBBP4	ENST00000765024.1		n.233+7708G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29616 AN: 151550 Hom.: 3051 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.195 AC: 29633 AN: 151668 Hom.: 3058 Cov.: 32 AF XY: 0.194 AC XY: 14392 AN XY: 74130

African (AFR) AF: 0.146 AC: 6037 AN: 41418

American (AMR) AF: 0.167 AC: 2537 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1198 AN: 3466

East Asian (EAS) AF: 0.140 AC: 722 AN: 5164

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4816

European-Finnish (FIN) AF: 0.206 AC: 2174 AN: 10554

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14726 AN: 67724

Other (OTH) AF: 0.230 AC: 484 AN: 2104

Alfa AF: 0.181 Hom.: 494

Bravo AF: 0.188

Asia WGS AF: 0.224 AC: 777 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.49
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17052344; hg19: chr17-21717543;