chr8-91070322-T-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The ENST00000285420.8(OTUD6B):​c.28T>A​(p.Trp10Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

OTUD6B
ENST00000285420.8 missense

Scores

5
12

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.68
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]
OTUD6B-AS1 (HGNC:50466): (OTUD6B antisense RNA 1 (head to head))

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1902782).
BP6
Variant 8-91070322-T-A is Benign according to our data. Variant chr8-91070322-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 3412773.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OTUD6BNM_016023.5 linkc.-63T>A upstream_gene_variant ENST00000404789.8 NP_057107.4 Q8N6M0-1A0A087X0W9
OTUD6BNM_001416022.1 linkc.-63T>A upstream_gene_variant NP_001402951.1
OTUD6BNM_001286745.3 linkc.-506T>A upstream_gene_variant NP_001273674.1 Q8N6M0-2
OTUD6BXM_047421864.1 linkc.-63T>A upstream_gene_variant XP_047277820.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OTUD6BENST00000404789.8 linkc.-63T>A upstream_gene_variant 1 NM_016023.5 ENSP00000384190.4 Q8N6M0-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1460080
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726122
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Benign:1
Sep 04, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.085
T
BayesDel_noAF
Benign
-0.36
CADD
Benign
17
DANN
Uncertain
0.97
DEOGEN2
Benign
0.013
T;T
Eigen
Uncertain
0.20
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Benign
0.35
T;.
M_CAP
Benign
0.028
D
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-0.86
T
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-0.12
.;N
REVEL
Benign
0.055
Sift
Benign
0.034
.;D
Sift4G
Uncertain
0.034
D;D
Vest4
0.25
MutPred
0.45
Gain of disorder (P = 0.0014);Gain of disorder (P = 0.0014);
MVP
0.43
MPC
0.023
ClinPred
0.56
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
gMVP
0.11

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: rs745687110; hg19: chr8-92082550; API