Variant 15-31483468-C-CGCGTCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4

The NM_001382637.1(OTUD7A):c.2627_2628insCGACGC(p.Asp875_Ala876dup) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.0000073 in 1,233,678 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000073 ( 0 hom. )

Consequence

OTUD7A
NM_001382637.1 inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.33

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 Uncertain_significance. Variant got 2 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001382637.1.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OTUD7A	NM_001382637.1 linkuse as main transcript	c.2627_2628insCGACGC	p.Asp875_Ala876dup	inframe_insertion	13/13	ENST00000307050.6
OTUD7A	NM_130901.3 linkuse as main transcript	c.2606_2607insCGACGC	p.Asp868_Ala869dup	inframe_insertion	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OTUD7A	ENST00000307050.6 linkuse as main transcript	c.2627_2628insCGACGC	p.Asp875_Ala876dup	inframe_insertion	13/13	1	NM_001382637.1	P2	Q8TE49-2
OTUD7A	ENST00000560598.2 linkuse as main transcript	c.2606_2607insCGACGC	p.Asp868_Ala869dup	inframe_insertion	14/14	5		A2	Q8TE49-1
OTUD7A	ENST00000678495.1 linkuse as main transcript	c.2606_2607insCGACGC	p.Asp868_Ala869dup	inframe_insertion	11/11			A2	Q8TE49-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000730

AC:

AN:

1233678

Hom.:

Cov.:

AF XY:

0.00000658

AC XY:

AN XY:

607772

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:

0.0000155

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000799

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Apr 26, 2022

Gene of Uncertain Significance -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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