Genetic Variant STUB1:c.-885_-789delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG (chr16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T) – ACMG Classification: Benign (-10 pts)

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 links:

STUB1-DT (HGNC:54519): (STUB1 divergent transcript)

STUB1-DT links:

Genome browser will be placed here

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 link	n.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
STUB1	ENST00000565677.5 link	c.-885_-789delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG	upstream_gene_variant	1	ENSP00000457228.1	Q9UNE7-2
STUB1-DT	ENST00000567091.1 link	n.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC	upstream_gene_variant	3
STUB1-DT	ENST00000571933.1 link	n.-305_-209delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC	upstream_gene_variant	6

Frequencies

GnomAD3 genomes

AF:

0.0363

AC:

2660

AN:

73218

Hom.:

164

Cov.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over