NM_015207.2:c.607-3037G>C

Variant names:

• chr1-19901230-G-C
• rs4654925
• NM_015207.2:c.607-3037G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015207.2(OTUD3):​c.607-3037G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,922 control chromosomes in the GnomAD database, including 15,902 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 0.45 (15902 hom., cov: 32)
• Consequence: OTUD3 NM_015207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 18 publications found

Genes affected

OTUD3 (HGNC:29038): (OTU deubiquitinase 3) Enables thiol-dependent deubiquitinase. Acts upstream of or within negative regulation of protein kinase B signaling; protein deubiquitination; and protein stabilization. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015207.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OTUD3	NM_015207.2	MANE Select	c.607-3037G>C		intron	N/A	NP_056022.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OTUD3	ENST00000375120.4	TSL:1 MANE Select	c.607-3037G>C		intron	N/A	ENSP00000364261.3
	OTUD3	ENST00000916791.1		c.607-3037G>C		intron	N/A	ENSP00000586850.1
	OTUD3	ENST00000880254.1		c.607-3037G>C		intron	N/A	ENSP00000550313.1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68861 AN: 151806 Hom.: 15873 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.454 AC: 68947 AN: 151922 Hom.: 15902 Cov.: 32 AF XY: 0.453 AC XY: 33663 AN XY: 74268

African (AFR) AF: 0.446 AC: 18485 AN: 41414

American (AMR) AF: 0.476 AC: 7269 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4816

European-Finnish (FIN) AF: 0.526 AC: 5535 AN: 10522

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32027 AN: 67954

Other (OTH) AF: 0.444 AC: 936 AN: 2108

Alfa AF: 0.432 Hom.: 7449

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		0.012
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4654925; hg19: chr1-20227723;