19-30009211-GTGATGATGATGATGA-GTGA
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_003796.3(URI1):c.909_920delTGATGATGATGA(p.Asp304_Asp307del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000389 in 1,541,428 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000029 ( 0 hom. )
Consequence
URI1
NM_003796.3 disruptive_inframe_deletion
NM_003796.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.01
Publications
17 publications found
Genes affected
URI1 (HGNC:13236): (URI1 prefoldin like chaperone) This gene encodes member of the prefoldin family of molecular chaperones. The encoded protein functions as a scaffolding protein and plays roles in ubiquitination and transcription, in part though interactions with the RNA polymerase II subunit RPB5. This gene may play a role in multiple malignancies including ovarian cancer and hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 22. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_003796.3
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003796.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| URI1 | MANE Select | c.909_920delTGATGATGATGA | p.Asp304_Asp307del | disruptive_inframe_deletion | Exon 8 of 11 | NP_003787.2 | O94763-1 | ||
| URI1 | c.855_866delTGATGATGATGA | p.Asp286_Asp289del | disruptive_inframe_deletion | Exon 8 of 11 | NP_001239570.1 | O94763-4 | |||
| URI1 | n.1183_1194delTGATGATGATGA | non_coding_transcript_exon | Exon 7 of 10 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| URI1 | TSL:1 MANE Select | c.909_920delTGATGATGATGA | p.Asp304_Asp307del | disruptive_inframe_deletion | Exon 8 of 11 | ENSP00000376097.2 | O94763-1 | ||
| URI1 | TSL:1 | c.855_866delTGATGATGATGA | p.Asp286_Asp289del | disruptive_inframe_deletion | Exon 8 of 11 | ENSP00000353817.4 | O94763-4 | ||
| URI1 | TSL:1 | n.*742_*753delTGATGATGATGA | non_coding_transcript_exon | Exon 7 of 10 | ENSP00000461003.1 | I3L467 |
Frequencies
GnomAD3 genomes 0.0000133 AC: 2AN: 150686Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
150686
Hom.:
Cov.:
0
Gnomad AFR
AF:
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000473 AC: 1AN: 211522 AF XY: 0.00000879 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
211522
AF XY:
Gnomad AFR exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000288 AC: 4AN: 1390742Hom.: 0 AF XY: 0.00000433 AC XY: 3AN XY: 692176 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1390742
Hom.:
AF XY:
AC XY:
3
AN XY:
692176
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32770
American (AMR)
AF:
AC:
0
AN:
42884
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24930
East Asian (EAS)
AF:
AC:
0
AN:
38196
South Asian (SAS)
AF:
AC:
2
AN:
82518
European-Finnish (FIN)
AF:
AC:
0
AN:
50318
Middle Eastern (MID)
AF:
AC:
0
AN:
5604
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1055886
Other (OTH)
AF:
AC:
0
AN:
57636
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.0000133 AC: 2AN: 150686Hom.: 0 Cov.: 0 AF XY: 0.0000136 AC XY: 1AN XY: 73480 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
150686
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
73480
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40896
American (AMR)
AF:
AC:
0
AN:
15106
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3456
East Asian (EAS)
AF:
AC:
0
AN:
5108
South Asian (SAS)
AF:
AC:
0
AN:
4748
European-Finnish (FIN)
AF:
AC:
0
AN:
10404
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
67696
Other (OTH)
AF:
AC:
0
AN:
2054
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational 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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