Variant 5-14600951-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_019018.3(OTULINL):c.65-13del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.056 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0062 ( 5 hom. )

Failed GnomAD Quality Control

Consequence

OTULINL
NM_019018.3 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.316

Variant links:

Genes affected

OTULINL (HGNC:25629): (OTU deubiquitinase with linear linkage specificity like) Located in cytoplasm. Is extrinsic component of endoplasmic reticulum membrane. Colocalizes with nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

OTULINL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 5-14600951-TG-T is Benign according to our data. Variant chr5-14600951-TG-T is described in ClinVar as [Benign]. Clinvar id is 402842.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
OTULINL	NM_019018.3 linkuse as main transcript	c.65-13del	splice_polypyrimidine_tract_variant, intron_variant	ENST00000274217.4	NP_061891.1
OTULINL	XM_047417322.1 linkuse as main transcript	c.-23-13del	splice_polypyrimidine_tract_variant, intron_variant		XP_047273278.1
OTULINL	XM_047417323.1 linkuse as main transcript	c.-23-13del	splice_polypyrimidine_tract_variant, intron_variant		XP_047273279.1
OTULINL	XR_925623.3 linkuse as main transcript	n.168-13del	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OTULINL	ENST00000274217.4 linkuse as main transcript	c.65-13del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_019018.3	ENSP00000274217	P1
OTULINL	ENST00000513825.1 linkuse as main transcript			upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

4181

AN:

75302

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0363

Gnomad AMI

AF:

0.0606

Gnomad AMR

AF:

0.0570

Gnomad ASJ

AF:

0.0778

Gnomad EAS

AF:

0.0573

Gnomad SAS

AF:

0.0591

Gnomad FIN

AF:

0.0269

Gnomad MID

AF:

0.0217

Gnomad NFE

AF:

0.0707

Gnomad OTH

AF:

0.0743

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00623

AC:

5933

AN:

951698

Hom.:

Cov.:

AF XY:

0.00679

AC XY:

3083

AN XY:

454180

show subpopulations

Gnomad4 AFR exome

AF:

0.00399

Gnomad4 AMR exome

AF:

0.0467

Gnomad4 ASJ exome

AF:

0.00716

Gnomad4 EAS exome

AF:

0.00784

Gnomad4 SAS exome

AF:

0.0357

Gnomad4 FIN exome

AF:

0.0133

Gnomad4 NFE exome

AF:

0.00476

Gnomad4 OTH exome

AF:

0.00474

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0555

AC:

4183

AN:

75332

Hom.:

Cov.:

AF XY:

0.0526

AC XY:

1940

AN XY:

36896

show subpopulations

Gnomad4 AFR

AF:

0.0363

Gnomad4 AMR

AF:

0.0572

Gnomad4 ASJ

AF:

0.0778

Gnomad4 EAS

AF:

0.0571

Gnomad4 SAS

AF:

0.0593

Gnomad4 FIN

AF:

0.0269

Gnomad4 NFE

AF:

0.0708

Gnomad4 OTH

AF:

0.0730

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over