chr15-31483468-C-CGCGTCG
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
NM_001382637.1 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.33
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 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 | c.2627_2628insCGACGC | p.Asp875_Ala876dup | inframe_insertion | 13/13 | ENST00000307050.6 | |
OTUD7A | NM_130901.3 | 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 | c.2627_2628insCGACGC | p.Asp875_Ala876dup | inframe_insertion | 13/13 | 1 | NM_001382637.1 | P2 | |
OTUD7A | ENST00000560598.2 | c.2606_2607insCGACGC | p.Asp868_Ala869dup | inframe_insertion | 14/14 | 5 | A2 | ||
OTUD7A | ENST00000678495.1 | c.2606_2607insCGACGC | p.Asp868_Ala869dup | inframe_insertion | 11/11 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000730 AC: 9AN: 1233678Hom.: 0 Cov.: 29 AF XY: 0.00000658 AC XY: 4AN XY: 607772
GnomAD4 exome
AF:
AC:
9
AN:
1233678
Hom.:
Cov.:
29
AF XY:
AC XY:
4
AN XY:
607772
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Bravo
AF:
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:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at