chr16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T

Variant names:

• chr16-679945-TGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG-T
• rs1567278451
• ENST00000880076.1:c.-580_-484delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000880076.1(STUB1):​c.-580_-484delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.036 (164 hom., cov: 0)
• Consequence: STUB1 ENST00000880076.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

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)

ENSG00000294321 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000880076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STUB1-DT	NR_136337.1		n.-265_-169delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STUB1	ENST00000880076.1		c.-580_-484delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG		5_prime_UTR	Exon 1 of 7	ENSP00000550135.1
	STUB1	ENST00000880076.1		c.-580_-484delGATGGGGCCGGCGGCTGGGGGCGGGGCCTCTGGATTGGGCGGCTGCTGGGGGCGGGGCCTCTGCGGATGGGGCCGGCTGCTGGGGGCGGGGCCTCTG		non_coding_transcript	N/A	ENSP00000550135.1
	STUB1-DT	ENST00000722587.1		n.164+119_164+215delCAGAGGCCCCGCCCCCAGCAGCCGGCCCCATCCGCAGAGGCCCCGCCCCCAGCAGCCGCCCAATCCAGAGGCCCCGCCCCCAGCCGCCGGCCCCATC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0363 AC: 2660 AN: 73218 Hom.: 164 Cov.: 0

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

African (AFR) AF: 0.124 AC: 2506 AN: 20180

American (AMR) AF: 0.0205 AC: 110 AN: 5372

Ashkenazi Jewish (ASJ) AF: 0.00181 AC: 4 AN: 2212

East Asian (EAS) AF: 0.000850 AC: 2 AN: 2354

South Asian (SAS) AF: 0.00217 AC: 4 AN: 1840

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2248

Middle Eastern (MID) AF: 0.00980 AC: 1 AN: 102

European-Non Finnish (NFE) AF: 0.000480 AC: 18 AN: 37478

Other (OTH) AF: 0.0209 AC: 20 AN: 958

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1567278451; hg19: chr16-729945;