Variant 21-46287136-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001314025.2(YBEY):c.210+13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,547,800 control chromosomes in the GnomAD database, including 155,095 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 12944 hom., cov: 30)

Exomes 𝑓: 0.44 ( 142151 hom. )

Consequence

YBEY
NM_001314025.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00700

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 Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 21-46287136-T-A is Benign according to our data. Variant chr21-46287136-T-A is described in ClinVar as [Benign]. Clinvar id is 403614.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YBEY	NM_001314025.2 linkuse as main transcript	c.210+13T>A		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+13T>A		intron_variant		2	NM_001314025.2	P1	P58557-1

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

60977

AN:

150198

Hom.:

12937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.466

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.394

GnomAD3 exomes

AF:

0.385

AC:

75237

AN:

195262

Hom.:

17263

AF XY:

0.383

AC XY:

40910

AN XY:

106768

show subpopulations

Gnomad AFR exome

AF:

0.257

Gnomad AMR exome

AF:

0.474

Gnomad ASJ exome

AF:

0.420

Gnomad EAS exome

AF:

0.261

Gnomad SAS exome

AF:

0.307

Gnomad FIN exome

AF:

0.441

Gnomad NFE exome

AF:

0.409

Gnomad OTH exome

AF:

0.404

GnomAD4 exome

AF:

0.443

AC:

618785

AN:

1397490

Hom.:

142151

Cov.:

AF XY:

0.439

AC XY:

304665

AN XY:

693860

show subpopulations

Gnomad4 AFR exome

AF:

0.275

Gnomad4 AMR exome

AF:

0.486

Gnomad4 ASJ exome

AF:

0.465

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.347

Gnomad4 FIN exome

AF:

0.464

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.432

GnomAD4 genome

AF:

0.406

AC:

61002

AN:

150310

Hom.:

12944

Cov.:

AF XY:

0.406

AC XY:

29797

AN XY:

73306

show subpopulations

Gnomad4 AFR

AF:

0.301

Gnomad4 AMR

AF:

0.470

Gnomad4 ASJ

AF:

0.466

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.456

Gnomad4 OTH

AF:

0.392

Alfa

AF:

0.0888

Hom.:

411

Bravo

AF:

0.404

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.80

DANN

Benign

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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