Variant 14-20448090-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

OSGEP (HGNC:):

OSGEP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 ClinVar 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 Lovd as [Benign].

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/exons	MANE	Protein	UniProt
OSGEP	NM_017807.4 linkuse as main transcript	c.702+16A>G		intron_variant		ENST00000206542.9	NP_060277.1	Q9NPF4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSGEP	ENST00000206542.9 linkuse as main transcript	c.702+16A>G		intron_variant		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

GnomAD3 exomes

AF:

0.256

AC:

64436

AN:

251336

Hom.:

8953

AF XY:

0.252

AC XY:

34297

AN XY:

135894

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 SAS exome

AF:

0.163

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

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.206

Gnomad4 EAS exome

AF:

0.108

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.326

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.272

GnomAD4 genome

AF:

0.295

AC:

44862

AN:

152002

Hom.:

6800

Cov.:

AF XY:

0.294

AC XY:

21834

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.204

Gnomad4 EAS

AF:

0.0858

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.331

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.263

Hom.:

3182

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.86

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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