8-91071247-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016023.5(OTUD6B):c.192A>G(p.Arg64=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
OTUD6B
NM_016023.5 synonymous
NM_016023.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.802
Genes affected
OTUD6B (HGNC:24281): (OTU deubiquitinase 6B) This gene encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Deubiquitinating enzymes are primarily involved in removing ubiquitin from proteins targeted for degradation. This protein may function as a negative regulator of the cell cycle in B cells. [provided by RefSeq, Nov 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 8-91071247-A-G is Benign according to our data. Variant chr8-91071247-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3053871.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.802 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTUD6B | NM_016023.5 | c.192A>G | p.Arg64= | synonymous_variant | 2/7 | ENST00000404789.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD6B | ENST00000404789.8 | c.192A>G | p.Arg64= | synonymous_variant | 2/7 | 1 | NM_016023.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152236Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250776Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135564
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461496Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727046
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GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74506
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
OTUD6B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 27, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
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