chr17-22190937-G-A

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Publications

5 publications found
Variant links:
Genes affected
UBBP4 (HGNC:12467): (ubiquitin B pseudogene 4)

Genome browser will be placed here

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
UBBP4NR_176224.1 linkn.349+7708G>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBBP4ENST00000648259.1 linkn.356+7708G>A intron_variant Intron 3 of 3
UBBP4ENST00000688301.2 linkn.245-13150G>A intron_variant Intron 1 of 1
UBBP4ENST00000765024.1 linkn.233+7708G>A intron_variant Intron 3 of 3
ENSG00000299617ENST00000765101.1 linkn.280+12327C>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.195
AC:
29616
AN:
151550
Hom.:
3051
Cov.:
32
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.:
32
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:
66
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
0
1230
2459
3689
4918
6148
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
324
648
972
1296
1620
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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
14
DANN
Benign
0.49
PhyloP100
0.21

Splicing

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

Publications

Other links and lift over

dbSNP: rs17052344; hg19: chr17-21717543; API