chr15-31489497-C-T

Position:

• chr15-31489497-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382637.1(OTUD7A):​c.1172-1931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,972 control chromosomes in the GnomAD database, including 5,048 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 0.26 (5048 hom., cov: 32)
• Consequence: OTUD7A NM_001382637.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTUD7A	NM_001382637.1	c.1172-1931G>A		intron_variant		ENST00000307050.6	NP_001369566.1
OTUD7A	NM_130901.3	c.1151-1931G>A		intron_variant			NP_570971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OTUD7A	ENST00000307050.6	c.1172-1931G>A		intron_variant		1	NM_001382637.1	ENSP00000305926	P2
OTUD7A	ENST00000560598.2	c.1151-1931G>A		intron_variant		5		ENSP00000453883	A2
OTUD7A	ENST00000678495.1	c.1151-1931G>A		intron_variant				ENSP00000503326	A2

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38961 AN: 151852 Hom.: 5046 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.256 AC: 38978 AN: 151972 Hom.: 5048 Cov.: 32 AF XY: 0.256 AC XY: 18994 AN XY: 74292

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.260

Alfa AF: 0.213 Hom.: 794

Bravo AF: 0.259

Asia WGS AF: 0.245 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs723623; hg19: chr15-31781700;