Genetic Variant NM_019018.3:c.65-13delG (chr5-14600951-TG-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_019018.3(OTULINL):c.65-13delG variant causes a 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 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.316

Publications

1 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -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 VariationId is 402842.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019018.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OTULINL	NM_019018.3	MANE Select	c.65-13delG		intron	N/A	NP_061891.1	Q9NUU6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OTULINL	ENST00000274217.4	TSL:1 MANE Select	c.65-13delG	intron	N/A	ENSP00000274217.3	Q9NUU6
OTULINL	ENST00000955069.1		c.65-43delG	intron	N/A	ENSP00000625127.1
OTULINL	ENST00000853045.1		c.65-13delG	intron	N/A	ENSP00000523104.1

Frequencies

GnomAD3 genomes

AF:

0.0555

AC:

4181

AN:

75302

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0295

AC:

884

AN:

29916

AF XY:

0.0341

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.0542

Gnomad ASJ exome

AF:

0.0235

Gnomad EAS exome

AF:

0.0475

Gnomad FIN exome

AF:

0.0540

Gnomad NFE exome

AF:

0.0233

Gnomad OTH exome

AF:

0.0150

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00399

AC:

AN:

21328

American (AMR)

AF:

0.0467

AC:

490

AN:

10498

Ashkenazi Jewish (ASJ)

AF:

0.00716

AC:

AN:

13404

East Asian (EAS)

AF:

0.00784

AC:

209

AN:

26652

South Asian (SAS)

AF:

0.0357

AC:

760

AN:

21310

European-Finnish (FIN)

AF:

0.0133

AC:

304

AN:

22898

Middle Eastern (MID)

AF:

0.00856

AC:

AN:

2688

European-Non Finnish (NFE)

AF:

0.00476

AC:

3780

AN:

793658

Other (OTH)

AF:

0.00474

AC:

186

AN:

39262

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.337

Heterozygous variant carriers

463

925

1388

1850

2313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

296

444

592

740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0363

AC:

841

AN:

23170

American (AMR)

AF:

0.0572

AC:

400

AN:

6998

Ashkenazi Jewish (ASJ)

AF:

0.0778

AC:

131

AN:

1684

East Asian (EAS)

AF:

0.0571

AC:

157

AN:

2750

South Asian (SAS)

AF:

0.0593

AC:

140

AN:

2360

European-Finnish (FIN)

AF:

0.0269

AC:

118

AN:

4388

Middle Eastern (MID)

AF:

0.0231

AC:

AN:

130

European-Non Finnish (NFE)

AF:

0.0708

AC:

2292

AN:

32390

Other (OTH)

AF:

0.0730

AC:

AN:

1000

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.290

Heterozygous variant carriers

318

637

955

1274

1592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.32

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over