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GeneBe

15-31483519-G-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001382637.1(OTUD7A):c.2577C>G(p.Thr859=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00159 in 1,388,544 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00077 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 7 hom. )

Consequence

OTUD7A
NM_001382637.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.519
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 15-31483519-G-C is Benign according to our data. Variant chr15-31483519-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3025916.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.519 with no splicing effect.
BS2
High AC in GnomAd at 115 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OTUD7ANM_001382637.1 linkuse as main transcriptc.2577C>G p.Thr859= synonymous_variant 13/13 ENST00000307050.6
OTUD7ANM_130901.3 linkuse as main transcriptc.2556C>G p.Thr852= synonymous_variant 14/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OTUD7AENST00000307050.6 linkuse as main transcriptc.2577C>G p.Thr859= synonymous_variant 13/131 NM_001382637.1 P2Q8TE49-2
OTUD7AENST00000560598.2 linkuse as main transcriptc.2556C>G p.Thr852= synonymous_variant 14/145 A2Q8TE49-1
OTUD7AENST00000678495.1 linkuse as main transcriptc.2556C>G p.Thr852= synonymous_variant 11/11 A2Q8TE49-1

Frequencies

GnomAD3 genomes
AF:
0.000774
AC:
115
AN:
148580
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000317
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000668
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00150
Gnomad OTH
AF:
0.000488
GnomAD3 exomes
AF:
0.000319
AC:
20
AN:
62722
Hom.:
0
AF XY:
0.000379
AC XY:
14
AN XY:
36970
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000803
Gnomad OTH exome
AF:
0.000548
GnomAD4 exome
AF:
0.00169
AC:
2090
AN:
1239858
Hom.:
7
Cov.:
29
AF XY:
0.00156
AC XY:
952
AN XY:
611326
show subpopulations
Gnomad4 AFR exome
AF:
0.000208
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000504
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00194
Gnomad4 OTH exome
AF:
0.00290
GnomAD4 genome
AF:
0.000773
AC:
115
AN:
148686
Hom.:
0
Cov.:
32
AF XY:
0.000662
AC XY:
48
AN XY:
72500
show subpopulations
Gnomad4 AFR
AF:
0.000316
Gnomad4 AMR
AF:
0.0000667
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00150
Gnomad4 OTH
AF:
0.000484
Bravo
AF:
0.000699

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2024OTUD7A: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
Cadd
Benign
10
Dann
Benign
0.88

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: rs759967630; hg19: chr15-31775722; API