Genetic Variant NM_001394757.1:c.445G>A (chr10-22209539-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394757.1(EBLN1):c.445G>A(p.Gly149Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,559,946 control chromosomes in the GnomAD database, including 44,016 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4630 hom., cov: 32)

Exomes 𝑓: 0.23 ( 39386 hom. )

Consequence

EBLN1
NM_001394757.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Publications

13 publications found

Variant links:

Genes affected

EBLN1 (HGNC:39430): (endogenous Bornavirus like nucleoprotein 1)

EBLN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005245656).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBLN1	NM_001394757.1 link	c.445G>A	p.Gly149Arg	missense_variant	Exon 3 of 3	ENST00000422359.3	NP_001381686.1
EBLN1	NM_001199938.2 link	c.445G>A	p.Gly149Arg	missense_variant	Exon 1 of 1		NP_001186867.1	P0CF75

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBLN1	ENST00000422359.3 link	c.445G>A	p.Gly149Arg	missense_variant	Exon 3 of 3	6	NM_001394757.1	ENSP00000473842.1		P0CF75

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

36934

AN:

149864

Hom.:

4621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.201

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.247

GnomAD2 exomes

AF:

0.229

AC:

37651

AN:

164578

AF XY:

0.222

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.244

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.234

AC:

329798

AN:

1409986

Hom.:

39386

Cov.:

AF XY:

0.231

AC XY:

161525

AN XY:

698394

show subpopulations

African (AFR)

AF:

0.267

AC:

8736

AN:

32728

American (AMR)

AF:

0.261

AC:

9924

AN:

38070

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

5985

AN:

25498

East Asian (EAS)

AF:

0.179

AC:

6792

AN:

38050

South Asian (SAS)

AF:

0.154

AC:

12673

AN:

82050

European-Finnish (FIN)

AF:

0.198

AC:

7044

AN:

35584

Middle Eastern (MID)

AF:

0.171

AC:

980

AN:

5728

European-Non Finnish (NFE)

AF:

0.241

AC:

263940

AN:

1093216

Other (OTH)

AF:

0.232

AC:

13724

AN:

59062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

17902

35804

53705

71607

89509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9058

18116

27174

36232

45290

<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:

0.246

AC:

36958

AN:

149960

Hom.:

4630

Cov.:

AF XY:

0.245

AC XY:

17975

AN XY:

73370

show subpopulations

African (AFR)

AF:

0.284

AC:

11208

AN:

39488

American (AMR)

AF:

0.270

AC:

4110

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.227

AC:

780

AN:

3442

East Asian (EAS)

AF:

0.201

AC:

1038

AN:

5176

South Asian (SAS)

AF:

0.163

AC:

785

AN:

4810

European-Finnish (FIN)

AF:

0.190

AC:

2002

AN:

10558

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.236

AC:

16054

AN:

67940

Other (OTH)

AF:

0.248

AC:

521

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1450

2899

4349

5798

7248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.237

Hom.:

14907

Bravo

AF:

0.253

TwinsUK

AF:

0.245

AC:

910

ALSPAC

AF:

0.232

AC:

895

ExAC

AF:

0.190

AC:

21643

Asia WGS

AF:

0.238

AC:

828

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.28

CADD

Benign

7.6

(source)

DANN

Benign

0.63

DEOGEN2

Benign

0.083

FATHMM_MKL

Benign

0.0024

LIST_S2

Benign

0.52

MetaRNN

Benign

0.0052

MutationAssessor

Benign

0.90

PhyloP100

0.010

PrimateAI

Benign

0.38

Sift4G

Benign

0.19

Vest4

0.089

MPC

0.65

GERP RS

0.51

Varity_R

0.095

gMVP

0.16

Mutation Taster

=100/0

polymorphism (auto)

(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