14-20448090-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017807.4(OSGEP):c.702+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,607,860 control chromosomes in the GnomAD database, including 68,291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6800 hom., cov: 32)

Exomes 𝑓: 0.28 ( 61491 hom. )

Consequence

OSGEP
NM_017807.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.947

Publications

28 publications found

Variant links:

Genes affected

OSGEP (HGNC:18028): (O-sialoglycoprotein endopeptidase) Predicted to enable N(6)-L-threonylcarbamoyladenine synthase activity and metal ion binding activity. Involved in tRNA threonylcarbamoyladenosine modification. Located in cytoplasm; nuclear speck; and plasma membrane. Part of EKC/KEOPS complex. Implicated in Galloway-Mowat syndrome 3. [provided by Alliance of Genome Resources, Apr 2022]

OSGEP Gene-Disease associations (from GenCC):

Galloway-Mowat syndrome 3
Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
Galloway-Mowat syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

OSGEP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 14-20448090-T-C is Benign according to our data. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20448090-T-C is described in CliVar as Benign. Clinvar id is 1165073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSGEP	NM_017807.4 link	c.702+16A>G		intron_variant	Intron 7 of 10	ENST00000206542.9	NP_060277.1	Q9NPF4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSGEP	ENST00000206542.9 link	c.702+16A>G		intron_variant	Intron 7 of 10	1	NM_017807.4	ENSP00000206542.4		Q9NPF4

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44788

AN:

151882

Hom.:

6792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.0860

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.297

GnomAD2 exomes

AF:

0.256

AC:

64436

AN:

251336

AF XY:

0.252

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.238

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.0789

Gnomad FIN exome

AF:

0.331

Gnomad NFE exome

AF:

0.294

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.285

AC:

414876

AN:

1455858

Hom.:

61491

Cov.:

AF XY:

0.281

AC XY:

203354

AN XY:

724686

show subpopulations

African (AFR)

AF:

0.338

AC:

11292

AN:

33362

American (AMR)

AF:

0.240

AC:

10740

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

5369

AN:

26104

East Asian (EAS)

AF:

0.108

AC:

4278

AN:

39680

South Asian (SAS)

AF:

0.164

AC:

14169

AN:

86154

European-Finnish (FIN)

AF:

0.326

AC:

17391

AN:

53410

Middle Eastern (MID)

AF:

0.200

AC:

1153

AN:

5758

European-Non Finnish (NFE)

AF:

0.302

AC:

334084

AN:

1106462

Other (OTH)

AF:

0.272

AC:

16400

AN:

60210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

14814

29627

44441

59254

74068

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10864

21728

32592

43456

54320

<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

AF:

0.295

AC:

44862

AN:

152002

Hom.:

6800

Cov.:

AF XY:

0.294

AC XY:

21834

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.342

AC:

14160

AN:

41448

American (AMR)

AF:

0.263

AC:

4010

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

707

AN:

3472

East Asian (EAS)

AF:

0.0858

AC:

444

AN:

5174

South Asian (SAS)

AF:

0.161

AC:

773

AN:

4814

European-Finnish (FIN)

AF:

0.331

AC:

3494

AN:

10562

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.300

AC:

20368

AN:

67954

Other (OTH)

AF:

0.296

AC:

623

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1642

3284

4926

6568

8210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.284

Hom.:

14294

Bravo

AF:

0.292

Asia WGS

AF:

0.155

AC:

540

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

May 13, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.86

(source)

DANN

Benign

0.62

PhyloP100

-0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over