15-31738494-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001382637.1(OTUD7A):c.-99-81417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 152,198 control chromosomes in the GnomAD database, including 129 homozygotes. 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: 𝑓 0.030 ( 129 hom., cov: 32)
Consequence
OTUD7A
NM_001382637.1 intron
NM_001382637.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0270
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTUD7A | NM_001382637.1 | c.-99-81417G>A | intron_variant | ENST00000307050.6 | NP_001369566.1 | |||
OTUD7A | NM_001329907.2 | c.-222-49013G>A | intron_variant | NP_001316836.1 | ||||
OTUD7A | NM_130901.3 | c.-222-49013G>A | intron_variant | NP_570971.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.-99-81417G>A | intron_variant | 1 | NM_001382637.1 | ENSP00000305926 | P2 | |||
OTUD7A | ENST00000558371.5 | n.73-49013G>A | intron_variant, non_coding_transcript_variant | 1 | ||||||
OTUD7A | ENST00000560598.2 | c.-222-49013G>A | intron_variant | 5 | ENSP00000453883 | A2 | ||||
OTUD7A | ENST00000560536.5 | c.-222-49013G>A | intron_variant, NMD_transcript_variant | 2 | ENSP00000453622 |
Frequencies
GnomAD3 genomes AF: 0.0303 AC: 4607AN: 152080Hom.: 128 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0303 AC: 4614AN: 152198Hom.: 129 Cov.: 32 AF XY: 0.0290 AC XY: 2156AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at