1-26282320-TCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4BA1
The NM_001389556.1(UBXN11):c.1464_1541del(p.Pro489_Gly514del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,031,132 control chromosomes in the GnomAD database, including 17 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.021 ( 0 hom., cov: 0)
Exomes 𝑓: 0.12 ( 17 hom. )
Failed GnomAD Quality Control
Consequence
UBXN11
NM_001389556.1 inframe_deletion
NM_001389556.1 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.21
Genes affected
UBXN11 (HGNC:30600): (UBX domain protein 11) This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001389556.1.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBXN11 | NM_001389556.1 | c.1464_1541del | p.Pro489_Gly514del | inframe_deletion | 15/15 | ENST00000374222.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBXN11 | ENST00000374222.6 | c.1464_1541del | p.Pro489_Gly514del | inframe_deletion | 15/15 | 5 | NM_001389556.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 836AN: 40336Hom.: 0 Cov.: 0 FAILED QC
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GnomAD4 exome AF: 0.117 AC: 120887AN: 1031132Hom.: 17 AF XY: 0.125 AC XY: 62790AN XY: 503740
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0209 AC: 843AN: 40402Hom.: 0 Cov.: 0 AF XY: 0.0220 AC XY: 435AN XY: 19744
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Small cell lung carcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Lung cancer Pathogenic:1
Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Hepatocellular carcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at