rs370428364

Positions:

• chr5-14600951-TG-T

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.316

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]

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTULINL	NM_019018.3	c.65-13del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000274217.4	NP_061891.1
OTULINL	XM_047417322.1	c.-23-13del		splice_polypyrimidine_tract_variant, intron_variant			XP_047273278.1
OTULINL	XM_047417323.1	c.-23-13del		splice_polypyrimidine_tract_variant, intron_variant			XP_047273279.1
OTULINL	XR_925623.3	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	c.65-13del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_019018.3	ENSP00000274217	P1
OTULINL	ENST00000513825.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 4181 AN: 75302 Hom.: 0 Cov.: 0 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.: 5 Cov.: 17 AF XY: 0.00679 AC XY: 3083 AN XY: 454180

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.: 0 Cov.: 0 AF XY: 0.0526 AC XY: 1940 AN XY: 36896

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

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

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: rs370428364; hg19: chr5-14601060; COSMIC: COSV57034061; COSMIC: COSV57034061;