15-31738494-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270
Variant links:
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
OTUD7ANM_001382637.1 linkuse as main transcriptc.-99-81417G>A intron_variant ENST00000307050.6 NP_001369566.1
OTUD7ANM_001329907.2 linkuse as main transcriptc.-222-49013G>A intron_variant NP_001316836.1
OTUD7ANM_130901.3 linkuse as main transcriptc.-222-49013G>A intron_variant NP_570971.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OTUD7AENST00000307050.6 linkuse as main transcriptc.-99-81417G>A intron_variant 1 NM_001382637.1 ENSP00000305926 P2Q8TE49-2
OTUD7AENST00000558371.5 linkuse as main transcriptn.73-49013G>A intron_variant, non_coding_transcript_variant 1
OTUD7AENST00000560598.2 linkuse as main transcriptc.-222-49013G>A intron_variant 5 ENSP00000453883 A2Q8TE49-1
OTUD7AENST00000560536.5 linkuse as main transcriptc.-222-49013G>A intron_variant, NMD_transcript_variant 2 ENSP00000453622

Frequencies

GnomAD3 genomes
AF:
0.0303
AC:
4607
AN:
152080
Hom.:
128
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0661
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0216
Gnomad ASJ
AF:
0.0254
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00290
Gnomad FIN
AF:
0.0114
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0184
Gnomad OTH
AF:
0.0296
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0303
AC:
4614
AN:
152198
Hom.:
129
Cov.:
32
AF XY:
0.0290
AC XY:
2156
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0661
Gnomad4 AMR
AF:
0.0216
Gnomad4 ASJ
AF:
0.0254
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00291
Gnomad4 FIN
AF:
0.0114
Gnomad4 NFE
AF:
0.0184
Gnomad4 OTH
AF:
0.0293
Alfa
AF:
0.0233
Hom.:
11
Bravo
AF:
0.0329
Asia WGS
AF:
0.00577
AC:
20
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.45
DANN
Benign
0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10519680; hg19: chr15-32030697; API