Variant 1-43164644-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_006824.3(EBNA1BP2):c.869A>T(p.Asn290Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,614,198 control chromosomes in the GnomAD database, including 127 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0061 ( 7 hom., cov: 32)

Exomes 𝑓: 0.011 ( 120 hom. )

Consequence

EBNA1BP2
NM_006824.3 missense, splice_region

Scores

Splicing: ADA: 0.9855

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.34

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 -12 ACMG points.

BP6

Variant 1-43164644-T-A is Benign according to our data. Variant chr1-43164644-T-A is described in ClinVar as [Benign]. Clinvar id is 789258.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
EBNA1BP2	NM_006824.3 linkuse as main transcript	c.869A>T	p.Asn290Ile	missense_variant, splice_region_variant	8/9	ENST00000236051.3	NP_006815.2
EBNA1BP2	NM_001159936.1 linkuse as main transcript	c.1034A>T	p.Asn345Ile	missense_variant, splice_region_variant	9/10		NP_001153408.1
EBNA1BP2	XM_047441489.1 linkuse as main transcript	c.869A>T	p.Asn290Ile	missense_variant, splice_region_variant	9/10		XP_047297445.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
EBNA1BP2	ENST00000236051.3 linkuse as main transcript	c.869A>T	p.Asn290Ile	missense_variant, splice_region_variant	8/9	1	NM_006824.3	ENSP00000236051	P1
EBNA1BP2	ENST00000431635.6 linkuse as main transcript	c.1034A>T	p.Asn345Ile	missense_variant, splice_region_variant	9/10	2		ENSP00000407323
EBNA1BP2	ENST00000463906.1 linkuse as main transcript	n.788A>T		splice_region_variant, non_coding_transcript_exon_variant	5/6	2

Frequencies

GnomAD3 genomes

AF:

0.00611

AC:

930

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00183

Gnomad AMI

AF:

0.00769

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.00188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0110

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00605

AC:

1521

AN:

251336

Hom.:

AF XY:

0.00626

AC XY:

850

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.00203

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00487

Gnomad FIN exome

AF:

0.00236

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.0106

AC:

15546

AN:

1461864

Hom.:

120

Cov.:

AF XY:

0.0105

AC XY:

7601

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00161

Gnomad4 AMR exome

AF:

0.00362

Gnomad4 ASJ exome

AF:

0.000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00468

Gnomad4 FIN exome

AF:

0.00275

Gnomad4 NFE exome

AF:

0.0128

Gnomad4 OTH exome

AF:

0.00849

GnomAD4 genome

AF:

0.00611

AC:

931

AN:

152334

Hom.:

Cov.:

AF XY:

0.00562

AC XY:

419

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.00183

Gnomad4 AMR

AF:

0.00300

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.00188

Gnomad4 NFE

AF:

0.0110

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00949

Hom.:

Bravo

AF:

0.00606

TwinsUK

AF:

0.0116

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.00942

AC:

ExAC

AF:

0.00597

AC:

725

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00981

EpiControl

AF:

0.00836

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.40

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Benign

0.055

T;T

Eigen

Uncertain

0.55

Eigen_PC

Uncertain

0.46

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.87

D;D

M_CAP

Pathogenic

0.44

MetaRNN

Benign

0.0092

T;T

MetaSVM

Benign

-0.44

MutationAssessor

Uncertain

2.4

.;M

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.48

PROVEAN

Pathogenic

-4.8

D;D

REVEL

Benign

0.26

Sift

Uncertain

0.0040

D;D

Sift4G

Benign

0.072

T;D

Polyphen

1.0

.;D

Vest4

0.53

MVP

0.76

MPC

1.2

ClinPred

0.019

GERP RS

4.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.93

gMVP

0.040

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.99

dbscSNV1_RF

Pathogenic

0.90

SpliceAI score (max)

0.060

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