Variant X-70063118-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_207320.3(OTUD6A):c.594C>T(p.Phe198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0041 in 1,209,759 control chromosomes in the GnomAD database, including 18 homozygotes. There are 1,617 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0043 ( 4 hom., 134 hem., cov: 23)

Exomes 𝑓: 0.0041 ( 14 hom. 1483 hem. )

Consequence

OTUD6A
NM_207320.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.128

Variant links:

Genes affected

OTUD6A (HGNC:32312): (OTU deubiquitinase 6A) Deubiquitinating enzymes (DUBs; see MIM 603478) are proteases that specifically cleave ubiquitin (MIM 191339) linkages, negating the action of ubiquitin ligases. DUBA2 belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain.[supplied by OMIM, May 2008]

OTUD6A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant X-70063118-C-T is Benign according to our data. Variant chrX-70063118-C-T is described in ClinVar as [Benign]. Clinvar id is 777743.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.128 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00408 (4475/1097876) while in subpopulation MID AF= 0.0268 (111/4137). AF 95% confidence interval is 0.0228. There are 14 homozygotes in gnomad4_exome. There are 1483 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OTUD6A	NM_207320.3 linkuse as main transcript	c.594C>T	p.Phe198=	synonymous_variant	1/1	ENST00000338352.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OTUD6A	ENST00000338352.3 linkuse as main transcript	c.594C>T	p.Phe198=	synonymous_variant	1/1		NM_207320.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00436

AC:

488

AN:

111831

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

136

AN XY:

33979

show subpopulations

Gnomad AFR

AF:

0.00422

Gnomad AMI

AF:

0.00742

Gnomad AMR

AF:

0.00460

Gnomad ASJ

AF:

0.00532

Gnomad EAS

AF:

0.000283

Gnomad SAS

AF:

0.00315

Gnomad FIN

AF:

0.000323

Gnomad MID

AF:

0.0211

Gnomad NFE

AF:

0.00505

Gnomad OTH

AF:

0.00401

GnomAD3 exomes

AF:

0.00405

AC:

740

AN:

182743

Hom.:

AF XY:

0.00398

AC XY:

268

AN XY:

67353

show subpopulations

Gnomad AFR exome

AF:

0.00411

Gnomad AMR exome

AF:

0.00452

Gnomad ASJ exome

AF:

0.00429

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000997

Gnomad FIN exome

AF:

0.000826

Gnomad NFE exome

AF:

0.00581

Gnomad OTH exome

AF:

0.00531

GnomAD4 exome

AF:

0.00408

AC:

4475

AN:

1097876

Hom.:

Cov.:

AF XY:

0.00408

AC XY:

1483

AN XY:

363286

show subpopulations

Gnomad4 AFR exome

AF:

0.00436

Gnomad4 AMR exome

AF:

0.00432

Gnomad4 ASJ exome

AF:

0.00464

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.00124

Gnomad4 FIN exome

AF:

0.00119

Gnomad4 NFE exome

AF:

0.00432

Gnomad4 OTH exome

AF:

0.00549

GnomAD4 genome

AF:

0.00432

AC:

483

AN:

111883

Hom.:

Cov.:

AF XY:

0.00394

AC XY:

134

AN XY:

34041

show subpopulations

Gnomad4 AFR

AF:

0.00411

Gnomad4 AMR

AF:

0.00459

Gnomad4 ASJ

AF:

0.00532

Gnomad4 EAS

AF:

0.000284

Gnomad4 SAS

AF:

0.00276

Gnomad4 FIN

AF:

0.000323

Gnomad4 NFE

AF:

0.00505

Gnomad4 OTH

AF:

0.00396

Alfa

AF:

0.00280

Hom.:

Bravo

AF:

0.00520

EpiCase

AF:

0.00840

EpiControl

AF:

0.00866

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 17, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.4

DANN

Benign

0.63

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