rs144158336
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_181503.3(EXOSC8):c.55-10_55-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00302 in 1,519,264 control chromosomes in the GnomAD database, including 106 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 48 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 58 hom. )
Consequence
EXOSC8
NM_181503.3 splice_polypyrimidine_tract, intron
NM_181503.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.35
Genes affected
EXOSC8 (HGNC:17035): (exosome component 8) This gene encodes a 3'-5' exoribonuclease that specifically interacts with mRNAs containing AU-rich elements. The encoded protein is part of the exosome complex that is important for the degradation of numerous RNA species. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 13-37002475-CAT-C is Benign according to our data. Variant chr13-37002475-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 235309.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0535 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOSC8 | NM_181503.3 | c.55-10_55-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000389704.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOSC8 | ENST00000389704.4 | c.55-10_55-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_181503.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0158 AC: 2404AN: 152034Hom.: 48 Cov.: 32
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GnomAD3 exomes AF: 0.00413 AC: 932AN: 225694Hom.: 29 AF XY: 0.00310 AC XY: 382AN XY: 123204
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GnomAD4 exome AF: 0.00160 AC: 2183AN: 1367112Hom.: 58 AF XY: 0.00146 AC XY: 997AN XY: 681922
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GnomAD4 genome ? AF: 0.0158 AC: 2409AN: 152152Hom.: 48 Cov.: 32 AF XY: 0.0156 AC XY: 1161AN XY: 74388
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 11, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Pontocerebellar hypoplasia, type 1C Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 13, 2022 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at