16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000565677.5(STUB1):c.-885_-789delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.036 ( 164 hom., cov: 0)
Consequence
STUB1
ENST00000565677.5 upstream_gene
ENST00000565677.5 upstream_gene
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.35
Genes affected
STUB1 (HGNC:11427): (STIP1 homology and U-box containing protein 1) This gene encodes a protein containing tetratricopeptide repeat and a U-box that functions as a ubiquitin ligase/cochaperone. The encoded protein binds to and ubiquitinates shock cognate 71 kDa protein (Hspa8) and DNA polymerase beta (Polb), among other targets. Mutations in this gene cause spinocerebellar ataxia, autosomal recessive 16. Alternative splicing results in multiple transcript variants. There is a pseudogene for this gene on chromosome 2. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T is Benign according to our data. Variant chr16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T is described in ClinVar as [Benign]. Clinvar id is 1526326.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STUB1-DT | NR_136337.1 | n.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STUB1 | ENST00000565677.5 | c.-885_-789delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG | upstream_gene_variant | 1 | ENSP00000457228.1 | |||||
STUB1-DT | ENST00000567091.1 | n.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC | upstream_gene_variant | 3 | ||||||
STUB1-DT | ENST00000571933.1 | n.-305_-209delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0363 AC: 2660AN: 73218Hom.: 164 Cov.: 0
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GnomAD4 genome AF: 0.0364 AC: 2665AN: 73232Hom.: 164 Cov.: 0 AF XY: 0.0360 AC XY: 1206AN XY: 33458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 28, 2022
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at