Variant rs58271568 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001314025.2(YBEY):c.210+10_210+12dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000047 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0041 ( 18 hom. )

Failed GnomAD Quality Control

Consequence

YBEY
NM_001314025.2 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.890

Variant links:

Genes affected

YBEY (HGNC:1299): (ybeY metalloendoribonuclease) This gene encodes a highly conserved metalloprotein. A similar protein in bacteria acts as an endoribonuclease, and is thought to function in ribosomal RNA maturation and ribosome assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

YBEY links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YBEY	NM_001314025.2 linkuse as main transcript	c.210+10_210+12dup		splice_region_variant, intron_variant		ENST00000397701.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YBEY	ENST00000397701.9 linkuse as main transcript	c.210+10_210+12dup		splice_region_variant, intron_variant		2	NM_001314025.2	P1	P58557-1

Frequencies

GnomAD3 genomes

AF:

0.0000469

AC:

AN:

149376

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000200

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000309

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0129

AC:

1751

AN:

136068

Hom.:

AF XY:

0.0131

AC XY:

970

AN XY:

74236

show subpopulations

Gnomad AFR exome

AF:

0.00496

Gnomad AMR exome

AF:

0.0156

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.00518

Gnomad SAS exome

AF:

0.0118

Gnomad FIN exome

AF:

0.0132

Gnomad NFE exome

AF:

0.0145

Gnomad OTH exome

AF:

0.0199

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00409

AC:

5523

AN:

1349072

Hom.:

Cov.:

AF XY:

0.00429

AC XY:

2867

AN XY:

668690

show subpopulations

Gnomad4 AFR exome

AF:

0.00173

Gnomad4 AMR exome

AF:

0.00826

Gnomad4 ASJ exome

AF:

0.00557

Gnomad4 EAS exome

AF:

0.00152

Gnomad4 SAS exome

AF:

0.00419

Gnomad4 FIN exome

AF:

0.00608

Gnomad4 NFE exome

AF:

0.00398

Gnomad4 OTH exome

AF:

0.00439

GnomAD4 genome

AF:

0.0000469

AC:

AN:

149376

Hom.:

Cov.:

AF XY:

0.0000964

AC XY:

AN XY:

72626

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000200

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000309

Gnomad4 NFE

AF:

0.0000148

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over