rs7164569
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001382637.1(OTUD7A):c.1134T>G(p.Leu378=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
OTUD7A
NM_001382637.1 synonymous
NM_001382637.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.41
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP7
?
Synonymous conserved (PhyloP=-1.41 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTUD7A | NM_001382637.1 | c.1134T>G | p.Leu378= | synonymous_variant | 10/13 | ENST00000307050.6 | |
OTUD7A | NM_130901.3 | c.1113T>G | p.Leu371= | synonymous_variant | 11/14 | ||
OTUD7A | NM_001329907.2 | c.1134T>G | p.Leu378= | synonymous_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.1134T>G | p.Leu378= | synonymous_variant | 10/13 | 1 | NM_001382637.1 | P2 | |
OTUD7A | ENST00000560598.2 | c.1113T>G | p.Leu371= | synonymous_variant | 11/14 | 5 | A2 | ||
OTUD7A | ENST00000678495.1 | c.1113T>G | p.Leu371= | synonymous_variant | 8/11 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251424Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135882
GnomAD3 exomes
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1
AN:
251424
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0
AN XY:
135882
Gnomad AFR exome
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GnomAD4 exome Cov.: 52
GnomAD4 exome
Cov.:
52
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at