Genetic Variant EOLA2:p.Glu132Glu (chrX-149932625-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001013845.2(EOLA2):c.396G>A(p.Glu132Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,203,711 control chromosomes in the GnomAD database, including 2 homozygotes. There are 55 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00072 ( 0 hom., 23 hem., cov: 19)

Exomes 𝑓: 0.000098 ( 2 hom. 32 hem. )

Consequence

EOLA2
NM_001013845.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.12

Publications

0 publications found

Variant links:

Genes affected

EOLA2 (HGNC:17402): (endothelium and lymphocyte associated ASCH domain 2)

EOLA2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant X-149932625-C-T is Benign according to our data. Variant chrX-149932625-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661626.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.12 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 23 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013845.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
EOLA2	NM_001013845.2	MANE Select	c.396G>A	p.Glu132Glu	synonymous	Exon 5 of 5	NP_001013867.1	Q96DE9
EOLA2	NM_001438792.1		c.396G>A	p.Glu132Glu	synonymous	Exon 5 of 5	NP_001425721.1
EOLA2	NM_001438793.1		c.396G>A	p.Glu132Glu	synonymous	Exon 5 of 5	NP_001425722.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
EOLA2	ENST00000370406.8	TSL:1 MANE Select	c.396G>A	p.Glu132Glu	synonymous	Exon 5 of 5	ENSP00000359434.3	Q96DE9
EOLA2	ENST00000355203.6	TSL:1	c.396G>A	p.Glu132Glu	synonymous	Exon 4 of 4	ENSP00000347339.2	Q96DE9
EOLA2	ENST00000370404.5	TSL:2	c.396G>A	p.Glu132Glu	synonymous	Exon 5 of 5	ENSP00000359432.1	Q96DE9

Frequencies

GnomAD3 genomes

AF:

0.000720

AC:

AN:

106996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00249

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000399

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00141

GnomAD2 exomes

AF:

0.000147

AC:

AN:

183454

AF XY:

0.0000589

show subpopulations

Gnomad AFR exome

AF:

0.00167

Gnomad AMR exome

AF:

0.0000729

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000244

Gnomad OTH exome

AF:

0.000221

GnomAD4 exome

AF:

0.0000976

AC:

107

AN:

1096715

Hom.:

Cov.:

AF XY:

0.0000884

AC XY:

AN XY:

362117

show subpopulations

African (AFR)

AF:

0.00251

AC:

AN:

26292

American (AMR)

AF:

0.000171

AC:

AN:

35177

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19382

East Asian (EAS)

AF:

0.00

AC:

AN:

30155

South Asian (SAS)

AF:

0.0000185

AC:

AN:

53938

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40526

Middle Eastern (MID)

AF:

0.000969

AC:

AN:

4129

European-Non Finnish (NFE)

AF:

0.0000119

AC:

AN:

841089

Other (OTH)

AF:

0.000435

AC:

AN:

46027

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.000720

AC:

AN:

106996

Hom.:

Cov.:

AF XY:

0.000777

AC XY:

AN XY:

29606

show subpopulations

African (AFR)

AF:

0.00249

AC:

AN:

28532

American (AMR)

AF:

0.000399

AC:

AN:

10036

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2620

East Asian (EAS)

AF:

0.00

AC:

AN:

3391

South Asian (SAS)

AF:

0.00

AC:

AN:

2404

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5474

Middle Eastern (MID)

AF:

0.00

AC:

AN:

233

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

52216

Other (OTH)

AF:

0.00141

AC:

AN:

1417

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.000214

Hom.:

Bravo

AF:

0.00110

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

5.4

(source)

DANN

Benign

0.89

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over