chr15-31483600-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001382637.1(OTUD7A):c.2496G>A(p.Ser832=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,223,872 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00067 ( 5 hom. )
Consequence
OTUD7A
NM_001382637.1 synonymous
NM_001382637.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.858
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 15-31483600-C-T is Benign according to our data. Variant chr15-31483600-C-T is described in ClinVar as [Benign]. Clinvar id is 3033632.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.858 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00783 (1166/148890) while in subpopulation AFR AF= 0.0272 (1121/41168). AF 95% confidence interval is 0.0259. There are 11 homozygotes in gnomad4. There are 522 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1168 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTUD7A | NM_001382637.1 | c.2496G>A | p.Ser832= | synonymous_variant | 13/13 | ENST00000307050.6 | |
OTUD7A | NM_130901.3 | c.2475G>A | p.Ser825= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.2496G>A | p.Ser832= | synonymous_variant | 13/13 | 1 | NM_001382637.1 | P2 | |
OTUD7A | ENST00000560598.2 | c.2475G>A | p.Ser825= | synonymous_variant | 14/14 | 5 | A2 | ||
OTUD7A | ENST00000678495.1 | c.2475G>A | p.Ser825= | synonymous_variant | 11/11 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00785 AC: 1168AN: 148788Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.000403 AC: 1AN: 2484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 1708
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GnomAD4 exome AF: 0.000671 AC: 721AN: 1074982Hom.: 5 Cov.: 28 AF XY: 0.000580 AC XY: 300AN XY: 516996
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GnomAD4 genome ? AF: 0.00783 AC: 1166AN: 148890Hom.: 11 Cov.: 32 AF XY: 0.00718 AC XY: 522AN XY: 72662
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
OTUD7A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at