chr15-31483519-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
NM_001382637.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.519
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 |
---|---|---|---|---|---|---|---|
OTUD7A | NM_001382637.1 | c.2577C>G | p.Thr859= | synonymous_variant | 13/13 | ENST00000307050.6 | |
OTUD7A | NM_130901.3 | c.2556C>G | p.Thr852= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.2577C>G | p.Thr859= | synonymous_variant | 13/13 | 1 | NM_001382637.1 | P2 | |
OTUD7A | ENST00000560598.2 | c.2556C>G | p.Thr852= | synonymous_variant | 14/14 | 5 | A2 | ||
OTUD7A | ENST00000678495.1 | c.2556C>G | p.Thr852= | synonymous_variant | 11/11 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000774 AC: 115AN: 148580Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000319 AC: 20AN: 62722Hom.: 0 AF XY: 0.000379 AC XY: 14AN XY: 36970
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GnomAD4 exome AF: 0.00169 AC: 2090AN: 1239858Hom.: 7 Cov.: 29 AF XY: 0.00156 AC XY: 952AN XY: 611326
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GnomAD4 genome ? AF: 0.000773 AC: 115AN: 148686Hom.: 0 Cov.: 32 AF XY: 0.000662 AC XY: 48AN XY: 72500
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | OTUD7A: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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