Variant 15-31483801-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001382637.1(OTUD7A):c.2295G>C(p.Val765=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 1,024,014 control chromosomes in the GnomAD database, including 247,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.76 ( 42596 hom., cov: 28)

Exomes 𝑓: 0.68 ( 205334 hom. )

Consequence

OTUD7A
NM_001382637.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.869

Variant links:

Genes affected

OTUD7A (HGNC:20718): (OTU deubiquitinase 7A) The protein encoded by this gene is a deubiquitinizing enzyme and possible tumor suppressor. The encoded protein acts on TNF receptor associated factor 6 (TRAF6) to control nuclear factor kappa B expression. However, this gene is downregulated by SNAIL1 in hepatocellular carcinoma cells, contributing to their progression and malignancy. [provided by RefSeq, Aug 2016]

OTUD7A links:

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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=-0.8).

BP6

Variant 15-31483801-C-G is Benign according to our data. Variant chr15-31483801-C-G is described in ClinVar as [Benign]. Clinvar id is 1227617.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.869 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTUD7A	NM_001382637.1 linkuse as main transcript	c.2295G>C	p.Val765=	synonymous_variant	13/13	ENST00000307050.6	NP_001369566.1
OTUD7A	NM_130901.3 linkuse as main transcript	c.2274G>C	p.Val758=	synonymous_variant	14/14		NP_570971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OTUD7A	ENST00000307050.6 linkuse as main transcript	c.2295G>C	p.Val765=	synonymous_variant	13/13	1	NM_001382637.1	ENSP00000305926	P2	Q8TE49-2
OTUD7A	ENST00000560598.2 linkuse as main transcript	c.2274G>C	p.Val758=	synonymous_variant	14/14	5		ENSP00000453883	A2	Q8TE49-1
OTUD7A	ENST00000678495.1 linkuse as main transcript	c.2274G>C	p.Val758=	synonymous_variant	11/11			ENSP00000503326	A2	Q8TE49-1

Frequencies

GnomAD3 genomes

AF:

0.756

AC:

109881

AN:

145254

Hom.:

42549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.916

Gnomad AMI

AF:

0.734

Gnomad AMR

AF:

0.755

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.922

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.711

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.753

GnomAD3 exomes

AF:

0.687

AC:

184

AN:

268

Hom.:

AF XY:

0.682

AC XY:

101

AN XY:

148

show subpopulations

Gnomad NFE exome

AF:

0.683

Gnomad OTH exome

AF:

0.833

GnomAD4 exome

AF:

0.682

AC:

599108

AN:

878658

Hom.:

205334

Cov.:

AF XY:

0.681

AC XY:

278710

AN XY:

409532

show subpopulations

Gnomad4 AFR exome

AF:

0.933

Gnomad4 AMR exome

AF:

0.760

Gnomad4 ASJ exome

AF:

0.698

Gnomad4 EAS exome

AF:

0.916

Gnomad4 SAS exome

AF:

0.580

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.676

Gnomad4 OTH exome

AF:

0.699

GnomAD4 genome

AF:

0.757

AC:

109977

AN:

145356

Hom.:

42596

Cov.:

AF XY:

0.752

AC XY:

53190

AN XY:

70702

show subpopulations

Gnomad4 AFR

AF:

0.916

Gnomad4 AMR

AF:

0.756

Gnomad4 ASJ

AF:

0.698

Gnomad4 EAS

AF:

0.922

Gnomad4 SAS

AF:

0.591

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.677

Gnomad4 OTH

AF:

0.754

Alfa

AF:

0.711

Hom.:

4789

Bravo

AF:

0.782

Asia WGS

AF:

0.730

AC:

1793

AN:

2456

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 02, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

OTUD7A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 06, 2022

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

-0.80

CADD

Benign

0.86

DANN

Benign

0.52

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