chr8-91071196-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_016023.5(OTUD6B):āc.141A>Gā(p.Gln47Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 1,612,418 control chromosomes in the GnomAD database, including 275,730 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.49 ( 20210 hom., cov: 31)
Exomes š: 0.59 ( 255520 hom. )
Consequence
OTUD6B
NM_016023.5 synonymous
NM_016023.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.532
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 8-91071196-A-G is Benign according to our data. Variant chr8-91071196-A-G is described in ClinVar as [Benign]. Clinvar id is 1259524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.532 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTUD6B | NM_016023.5 | c.141A>G | p.Gln47Gln | synonymous_variant | Exon 2 of 7 | ENST00000404789.8 | NP_057107.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.495 AC: 75080AN: 151812Hom.: 20209 Cov.: 31
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GnomAD3 exomes AF: 0.540 AC: 135535AN: 250798Hom.: 38500 AF XY: 0.560 AC XY: 75869AN XY: 135550
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GnomAD4 exome AF: 0.586 AC: 856354AN: 1460488Hom.: 255520 Cov.: 37 AF XY: 0.591 AC XY: 429222AN XY: 726560
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GnomAD4 genome AF: 0.494 AC: 75088AN: 151930Hom.: 20210 Cov.: 31 AF XY: 0.496 AC XY: 36832AN XY: 74246
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Aug 14, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies Benign:1
Sep 05, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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