Genetic Variant UBBP4:n.356+7708G>A (chr17-22190937-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648259.1(UBBP4):n.356+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
ENST00000648259.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Publications

5 publications found

Variant links:

Genes affected

UBBP4 (HGNC:):

UBBP4 links:

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

UBBP4 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBBP4	NR_176224.1 link	n.349+7708G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
UBBP4	ENST00000648259.1 link	n.356+7708G>A	intron_variant	Intron 3 of 3
UBBP4	ENST00000688301.2 link	n.245-13150G>A	intron_variant	Intron 1 of 1
UBBP4	ENST00000765024.1 link	n.233+7708G>A	intron_variant	Intron 3 of 3
ENSG00000299617	ENST00000765101.1 link	n.280+12327C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29616

AN:

151550

Hom.:

3051

Cov.:

show subpopulations

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.:

AF XY:

0.194

AC XY:

14392

AN XY:

74130

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.217

AC:

14726

AN:

67724

Other (OTH)

AF:

0.230

AC:

484

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1230

2459

3689

4918

6148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.49

PhyloP100

0.21

Splicing

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

Publications

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chr17-22190937-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over