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GeneBe

8-91071196-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_016023.5(OTUD6B):c.141A>G(p.Gln47=) 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 (★★).

Frequency

Genomes: 𝑓 0.49 ( 20210 hom., cov: 31)
Exomes 𝑓: 0.59 ( 255520 hom. )

Consequence

OTUD6B
NM_016023.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.532
Variant links:
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.532 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
OTUD6BNM_016023.5 linkuse as main transcriptc.141A>G p.Gln47= synonymous_variant 2/7 ENST00000404789.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OTUD6BENST00000404789.8 linkuse as main transcriptc.141A>G p.Gln47= synonymous_variant 2/71 NM_016023.5 Q8N6M0-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.495
AC:
75080
AN:
151812
Hom.:
20209
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.286
Gnomad AMI
AF:
0.625
Gnomad AMR
AF:
0.420
Gnomad ASJ
AF:
0.538
Gnomad EAS
AF:
0.553
Gnomad SAS
AF:
0.668
Gnomad FIN
AF:
0.578
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.603
Gnomad OTH
AF:
0.528
GnomAD3 exomes
AF:
0.540
AC:
135535
AN:
250798
Hom.:
38500
AF XY:
0.560
AC XY:
75869
AN XY:
135550
show subpopulations
Gnomad AFR exome
AF:
0.277
Gnomad AMR exome
AF:
0.334
Gnomad ASJ exome
AF:
0.548
Gnomad EAS exome
AF:
0.557
Gnomad SAS exome
AF:
0.653
Gnomad FIN exome
AF:
0.578
Gnomad NFE exome
AF:
0.598
Gnomad OTH exome
AF:
0.571
GnomAD4 exome
AF:
0.586
AC:
856354
AN:
1460488
Hom.:
255520
Cov.:
37
AF XY:
0.591
AC XY:
429222
AN XY:
726560
show subpopulations
Gnomad4 AFR exome
AF:
0.268
Gnomad4 AMR exome
AF:
0.347
Gnomad4 ASJ exome
AF:
0.545
Gnomad4 EAS exome
AF:
0.550
Gnomad4 SAS exome
AF:
0.651
Gnomad4 FIN exome
AF:
0.578
Gnomad4 NFE exome
AF:
0.603
Gnomad4 OTH exome
AF:
0.582
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.494
AC:
75088
AN:
151930
Hom.:
20210
Cov.:
31
AF XY:
0.496
AC XY:
36832
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.286
Gnomad4 AMR
AF:
0.420
Gnomad4 ASJ
AF:
0.538
Gnomad4 EAS
AF:
0.552
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.578
Gnomad4 NFE
AF:
0.603
Gnomad4 OTH
AF:
0.531
Alfa
AF:
0.559
Hom.:
12302
Bravo
AF:
0.467
Asia WGS
AF:
0.617
AC:
2144
AN:
3478
EpiCase
AF:
0.602
EpiControl
AF:
0.608

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 05, 2021- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 14, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
8.6
Dann
Benign
0.52
RBP_binding_hub_radar
1.0
RBP_regulation_power_radar
3.8

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11557571; hg19: chr8-92083424; COSMIC: COSV53442181; COSMIC: COSV53442181; API