17-44207332-CTCG-CTCGTCG
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3
The NM_014233.4(UBTF):c.2202_2204dupCGA(p.Asp734dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.000000685 in 1,460,400 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
UBTF
NM_014233.4 disruptive_inframe_insertion
NM_014233.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.02
Publications
0 publications found
Genes affected
UBTF (HGNC:12511): (upstream binding transcription factor) This gene encodes a member of the HMG-box DNA-binding protein family. The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3, 11 and X and the long arm of chromosome 11. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_014233.4
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014233.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| UBTF | NM_014233.4 | MANE Select | c.2202_2204dupCGA | p.Asp734dup | disruptive_inframe_insertion | Exon 21 of 21 | NP_055048.1 | P17480-1 | |
| UBTF | NM_001076683.2 | c.2091_2093dupCGA | p.Asp697dup | disruptive_inframe_insertion | Exon 20 of 20 | NP_001070151.1 | P17480-2 | ||
| UBTF | NM_001076684.3 | c.2091_2093dupCGA | p.Asp697dup | disruptive_inframe_insertion | Exon 20 of 20 | NP_001070152.1 | P17480-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| UBTF | ENST00000436088.6 | TSL:2 MANE Select | c.2202_2204dupCGA | p.Asp734dup | disruptive_inframe_insertion | Exon 21 of 21 | ENSP00000390669.1 | P17480-1 | |
| UBTF | ENST00000529383.5 | TSL:1 | c.2202_2204dupCGA | p.Asp734dup | disruptive_inframe_insertion | Exon 20 of 20 | ENSP00000435708.1 | P17480-1 | |
| UBTF | ENST00000343638.9 | TSL:1 | c.2091_2093dupCGA | p.Asp697dup | disruptive_inframe_insertion | Exon 20 of 20 | ENSP00000345297.5 | P17480-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460400Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726358 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1460400
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
726358
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33440
American (AMR)
AF:
AC:
0
AN:
44446
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26054
East Asian (EAS)
AF:
AC:
0
AN:
39642
South Asian (SAS)
AF:
AC:
0
AN:
85940
European-Finnish (FIN)
AF:
AC:
0
AN:
53370
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111392
Other (OTH)
AF:
AC:
0
AN:
60350
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
30
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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