rs1320150

Positions:

• chr14-20451884-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_017807.4(OSGEP):​c.411+90G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 1,185,608 control chromosomes in the GnomAD database, including 207,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.59 (26667 hom., cov: 33)
  • Exomes 𝑓: 0.59 (180522 hom.)
• Consequence: OSGEP NM_017807.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.31

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 14-20451884-C-T is Benign according to our data. Variant chr14-20451884-C-T is described in ClinVar as [Benign]. Clinvar id is 1284155.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSGEP	NM_017807.4	c.411+90G>A		intron_variant		ENST00000206542.9	NP_060277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSGEP	ENST00000206542.9	c.411+90G>A		intron_variant		1	NM_017807.4	ENSP00000206542	P1
	ENST00000555435.1	n.444C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89722 AN: 151996 Hom.: 26629 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.622

GnomAD4 exome AF: 0.588 AC: 608155 AN: 1033494 Hom.: 180522 Cov.: 13 AF XY: 0.588 AC XY: 301684 AN XY: 512762

Gnomad4 AFR exome AF: 0.590

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.643

Gnomad4 EAS exome AF: 0.499

Gnomad4 SAS exome AF: 0.558

Gnomad4 FIN exome AF: 0.675

Gnomad4 NFE exome AF: 0.592

Gnomad4 OTH exome AF: 0.596

GnomAD4 genome AF: 0.591 AC: 89826 AN: 152114 Hom.: 26667 Cov.: 33 AF XY: 0.593 AC XY: 44117 AN XY: 74366

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.622

Alfa AF: 0.586 Hom.: 3263

Bravo AF: 0.577

Asia WGS AF: 0.540 AC: 1881 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.80
CADD	Benign	2.3
DANN	Benign	0.79

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: rs1320150; hg19: chr14-20920043;