Variant chr1-43171575-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_006824.3(EBNA1BP2):c.227C>G(p.Pro76Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00753 in 1,614,084 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0073 ( 10 hom., cov: 32)

Exomes 𝑓: 0.0076 ( 70 hom. )

Consequence

EBNA1BP2
NM_006824.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.91

Variant links:

Genes affected

EBNA1BP2 (HGNC:15531): (EBNA1 binding protein 2) Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal large subunit biogenesis. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

EBNA1BP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009445906).

BP6

Variant 1-43171575-G-C is Benign according to our data. Variant chr1-43171575-G-C is described in ClinVar as [Benign]. Clinvar id is 777906.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
EBNA1BP2	NM_006824.3 linkuse as main transcript	c.227C>G	p.Pro76Arg	missense_variant	3/9	ENST00000236051.3
EBNA1BP2	NM_001159936.1 linkuse as main transcript	c.392C>G	p.Pro131Arg	missense_variant	4/10
EBNA1BP2	XM_047441489.1 linkuse as main transcript	c.227C>G	p.Pro76Arg	missense_variant	4/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBNA1BP2	ENST00000236051.3 linkuse as main transcript	c.227C>G	p.Pro76Arg	missense_variant	3/9	1	NM_006824.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00732

AC:

1113

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00332

Gnomad FIN

AF:

0.0245

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00652

AC:

1640

AN:

251424

Hom.:

AF XY:

0.00620

AC XY:

843

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00127

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00369

Gnomad FIN exome

AF:

0.0197

Gnomad NFE exome

AF:

0.00862

Gnomad OTH exome

AF:

0.00733

GnomAD4 exome

AF:

0.00756

AC:

11045

AN:

1461866

Hom.:

Cov.:

AF XY:

0.00743

AC XY:

5406

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00378

Gnomad4 FIN exome

AF:

0.0181

Gnomad4 NFE exome

AF:

0.00822

Gnomad4 OTH exome

AF:

0.00709

GnomAD4 genome

AF:

0.00731

AC:

1113

AN:

152218

Hom.:

Cov.:

AF XY:

0.00802

AC XY:

597

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.0245

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00992

Hom.:

Bravo

AF:

0.00465

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00727

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.00721

AC:

ExAC

AF:

0.00633

AC:

768

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00883

EpiControl

AF:

0.00705

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.25

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.060

T;T

Eigen

Uncertain

0.48

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.80

T;T

MetaRNN

Benign

0.0094

T;T

MetaSVM

Benign

-0.61

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.55

PROVEAN

Pathogenic

-7.0

D;D

REVEL

Uncertain

0.33

Sift

Uncertain

0.0020

D;D

Sift4G

Uncertain

0.0050

D;D

Polyphen

1.0

.;D

Vest4

0.48

MVP

0.76

MPC

0.63

ClinPred

0.098

GERP RS

5.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.73

gMVP

0.33

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