Variant chr10-23439541-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_001145373.3(OTUD1):c.84C>T(p.Ala28Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00845 in 1,380,678 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0086 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0084 ( 88 hom. )

Consequence

OTUD1
NM_001145373.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.781

Variant links:

Genes affected

OTUD1 (HGNC:27346): (OTU deubiquitinase 1) Deubiquitinating enzymes (DUBs; see MIM 603478) are proteases that specifically cleave ubiquitin (MIM 191339) linkages, negating the action of ubiquitin ligases. DUBA7 belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain.[supplied by OMIM, May 2008]

OTUD1 links:

ENSG00000287124 (HGNC:):

ENSG00000287124 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 10-23439541-C-T is Benign according to our data. Variant chr10-23439541-C-T is described in ClinVar as [Benign]. Clinvar id is 3037482.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.781 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTUD1	NM_001145373.3 linkuse as main transcript	c.84C>T	p.Ala28Ala	synonymous_variant	1/1	ENST00000376495.5	NP_001138845.1	Q5VV17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OTUD1	ENST00000376495.5 linkuse as main transcript	c.84C>T	p.Ala28Ala	synonymous_variant	1/1	6	NM_001145373.3	ENSP00000365678.3		Q5VV17
ENSG00000287124	ENST00000702412.1 linkuse as main transcript	n.88+496C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00863

AC:

1304

AN:

151026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00414

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.0213

Gnomad ASJ

AF:

0.0258

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00644

Gnomad FIN

AF:

0.000781

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.00880

Gnomad OTH

AF:

0.0208

GnomAD3 exomes

AF:

0.00957

AC:

471

AN:

49220

Hom.:

AF XY:

0.00899

AC XY:

262

AN XY:

29150

show subpopulations

Gnomad AFR exome

AF:

0.00836

Gnomad AMR exome

AF:

0.00900

Gnomad ASJ exome

AF:

0.0222

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00505

Gnomad FIN exome

AF:

0.000869

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.0209

GnomAD4 exome

AF:

0.00843

AC:

10360

AN:

1229542

Hom.:

Cov.:

AF XY:

0.00851

AC XY:

5148

AN XY:

605038

show subpopulations

Gnomad4 AFR exome

AF:

0.00579

Gnomad4 AMR exome

AF:

0.0113

Gnomad4 ASJ exome

AF:

0.0227

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00525

Gnomad4 FIN exome

AF:

0.00108

Gnomad4 NFE exome

AF:

0.00843

Gnomad4 OTH exome

AF:

0.0123

GnomAD4 genome

AF:

0.00862

AC:

1303

AN:

151136

Hom.:

Cov.:

AF XY:

0.00842

AC XY:

622

AN XY:

73854

show subpopulations

Gnomad4 AFR

AF:

0.00413

Gnomad4 AMR

AF:

0.0212

Gnomad4 ASJ

AF:

0.0258

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00644

Gnomad4 FIN

AF:

0.000781

Gnomad4 NFE

AF:

0.00880

Gnomad4 OTH

AF:

0.0206

Alfa

AF:

0.00230

Hom.:

Bravo

AF:

0.0105

Asia WGS

AF:

0.00204

AC:

AN:

3442

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OTUD1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

7.1

DANN

Benign

0.94

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over