chr16-680830-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005861.4(STUB1):c.159+146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 751,636 control chromosomes in the GnomAD database, including 24,957 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5595 hom., cov: 27)
Exomes 𝑓: 0.23 ( 19362 hom. )
Consequence
STUB1
NM_005861.4 intron
NM_005861.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.959
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 16-680830-C-T is Benign according to our data. Variant chr16-680830-C-T is described in ClinVar as [Benign]. Clinvar id is 1295562.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STUB1 | NM_005861.4 | c.159+146C>T | intron_variant | ENST00000219548.9 | |||
STUB1 | NM_001293197.2 | c.-147+146C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STUB1 | ENST00000219548.9 | c.159+146C>T | intron_variant | 1 | NM_005861.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 37372AN: 147116Hom.: 5590 Cov.: 27
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GnomAD4 exome AF: 0.233 AC: 140895AN: 604420Hom.: 19362 Cov.: 9 AF XY: 0.234 AC XY: 68682AN XY: 293394
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GnomAD4 genome AF: 0.254 AC: 37400AN: 147216Hom.: 5595 Cov.: 27 AF XY: 0.266 AC XY: 19095AN XY: 71764
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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
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 25, 2019 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at