rs1567278480

Variant names:

• chr16-679958-GGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT-G
• rs1567278480
• ENST00000565677.5:c.-872_-808delGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000565677.5(STUB1):​c.-872_-808delGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT 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 0.034 (148 hom., cov: 0)
• Consequence: STUB1 ENST00000565677.5 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.66

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)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-679958-GGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT-G is Benign according to our data. Variant chr16-679958-GGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT-G is described in ClinVar as [Benign]. Clinvar id is 1281841.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STUB1-DT	NR_136337.1	n.-246_-182delAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STUB1	ENST00000565677.5	c.-872_-808delGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCT		upstream_gene_variant		1		ENSP00000457228.1
STUB1-DT	ENST00000567091.1	n.-246_-182delAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGC		upstream_gene_variant		3
STUB1-DT	ENST00000571933.1	n.-286_-222delAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGC		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 4454 AN: 129984 Hom.: 149 Cov.: 0

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.0321

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0276

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0309

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0343 AC: 4457 AN: 130052 Hom.: 148 Cov.: 0 AF XY: 0.0327 AC XY: 2081 AN XY: 63614

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0121

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0112 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567278480; hg19: chr16-729958;