dbSNP rs3832186: EBLN2:p.Arg84LysfsTer18 (chr3-73062330-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018029.4(EBLN2):c.250dupA(p.Arg84LysfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,607,514 control chromosomes in the GnomAD database, including 17,201 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1549 hom., cov: 30)

Exomes 𝑓: 0.13 ( 15652 hom. )

Consequence

EBLN2
NM_018029.4 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

4 publications found

Variant links:

Genes affected

EBLN2 (HGNC:25493): (endogenous Bornavirus like nucleoprotein 2)

EBLN2 links:

PPP4R2 (HGNC:18296): (protein phosphatase 4 regulatory subunit 2) The protein encoded by this gene is a regulatory subunit of the serine/threonine-protein phosphatase 4 complex. In addition to being required for efficient DNA double strand break repair, this complex plays a role in organization of microtubules at centrosomes and processing of spliceosomal snRNPs. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

PPP4R2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBLN2	NM_018029.4 link	c.250dupA	p.Arg84LysfsTer18	frameshift_variant	Exon 1 of 1	ENST00000533473.1	NP_060499.3	Q6P2I7
PPP4R2	NM_174907.4 link	c.419+1271dupA		intron_variant	Intron 5 of 8	ENST00000356692.10	NP_777567.1	Q9NY27-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBLN2	ENST00000533473.1 link	c.250dupA	p.Arg84LysfsTer18	frameshift_variant	Exon 1 of 1	6	NM_018029.4	ENSP00000432104.1		Q6P2I7
PPP4R2	ENST00000356692.10 link	c.419+1271dupA		intron_variant	Intron 5 of 8	1	NM_174907.4	ENSP00000349124.5		Q9NY27-1

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19605

AN:

152038

Hom.:

1549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.0894

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.128

GnomAD2 exomes

AF:

0.148

AC:

34705

AN:

235026

AF XY:

0.155

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0953

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.0832

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.149

GnomAD4 exome

AF:

0.129

AC:

187598

AN:

1455358

Hom.:

15652

Cov.:

AF XY:

0.135

AC XY:

98066

AN XY:

723838

show subpopulations

African (AFR)

AF:

0.107

AC:

3538

AN:

33054

American (AMR)

AF:

0.100

AC:

4272

AN:

42706

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

4557

AN:

25918

East Asian (EAS)

AF:

0.344

AC:

13609

AN:

39602

South Asian (SAS)

AF:

0.325

AC:

27640

AN:

85024

European-Finnish (FIN)

AF:

0.0902

AC:

4801

AN:

53242

Middle Eastern (MID)

AF:

0.265

AC:

1520

AN:

5730

European-Non Finnish (NFE)

AF:

0.107

AC:

118489

AN:

1110006

Other (OTH)

AF:

0.153

AC:

9172

AN:

60076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

9048

18095

27143

36190

45238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4532

9064

13596

18128

22660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.129

AC:

19630

AN:

152156

Hom.:

1549

Cov.:

AF XY:

0.132

AC XY:

9829

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.108

AC:

4504

AN:

41526

American (AMR)

AF:

0.119

AC:

1820

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3472

East Asian (EAS)

AF:

0.363

AC:

1873

AN:

5162

South Asian (SAS)

AF:

0.336

AC:

1617

AN:

4816

European-Finnish (FIN)

AF:

0.0894

AC:

945

AN:

10570

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7824

AN:

68002

Other (OTH)

AF:

0.131

AC:

276

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

835

1669

2504

3338

4173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.131

Hom.:

1044

Bravo

AF:

0.125

Asia WGS

AF:

0.341

AC:

1186

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.35

Mutation Taster

=26/74

disease causing

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over