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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.35
Variant links:
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]
STUB1-DT (HGNC:54519): (STUB1 divergent transcript)

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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-DTNR_136337.1 linkn.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STUB1ENST00000565677.5 linkc.-885_-789delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG upstream_gene_variant 1 ENSP00000457228.1 Q9UNE7-2
STUB1-DTENST00000567091.1 linkn.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC upstream_gene_variant 3
STUB1-DTENST00000571933.1 linkn.-305_-209delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.0363
AC:
2660
AN:
73218
Hom.:
164
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0205
Gnomad ASJ
AF:
0.00181
Gnomad EAS
AF:
0.000847
Gnomad SAS
AF:
0.00217
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0175
Gnomad NFE
AF:
0.000480
Gnomad OTH
AF:
0.0211
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0364
AC:
2665
AN:
73232
Hom.:
164
Cov.:
0
AF XY:
0.0360
AC XY:
1206
AN XY:
33458
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.0205
Gnomad4 ASJ
AF:
0.00181
Gnomad4 EAS
AF:
0.000850
Gnomad4 SAS
AF:
0.00217
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000480
Gnomad4 OTH
AF:
0.0209

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1567278451; hg19: chr16-729945; API