Genetic Variant EML2:c.*14G>A (chr19-45609649-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_012155.4(EML2):c.*14G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,590,846 control chromosomes in the GnomAD database, including 2,650 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.077 ( 1018 hom., cov: 31)

Exomes 𝑓: 0.029 ( 1632 hom. )

Consequence

EML2
NM_012155.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

5 publications found

Variant links:

Genes affected

EML2 (HGNC:18035): (EMAP like 2) Enables microtubule binding activity. Involved in negative regulation of microtubule polymerization and regulation of microtubule nucleation. Colocalizes with mitotic spindle. [provided by Alliance of Genome Resources, Apr 2022]

EML2 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 (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EML2	NM_012155.4 link	c.*14G>A		3_prime_UTR_variant	Exon 19 of 19	ENST00000245925.8	NP_036287.1	O95834-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML2	ENST00000245925.8 link	c.*14G>A		3_prime_UTR_variant	Exon 19 of 19	1	NM_012155.4	ENSP00000245925.3		O95834-1

Frequencies

GnomAD3 genomes

AF:

0.0768

AC:

11649

AN:

151778

Hom.:

1015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0418

Gnomad ASJ

AF:

0.0338

Gnomad EAS

AF:

0.0371

Gnomad SAS

AF:

0.0965

Gnomad FIN

AF:

0.00717

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0196

Gnomad OTH

AF:

0.0722

GnomAD2 exomes

AF:

0.0434

AC:

10131

AN:

233640

AF XY:

0.0432

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.0195

Gnomad ASJ exome

AF:

0.0360

Gnomad EAS exome

AF:

0.0331

Gnomad FIN exome

AF:

0.00713

Gnomad NFE exome

AF:

0.0199

Gnomad OTH exome

AF:

0.0377

GnomAD4 exome

AF:

0.0294

AC:

42253

AN:

1438952

Hom.:

1632

Cov.:

AF XY:

0.0311

AC XY:

22215

AN XY:

714932

show subpopulations

African (AFR)

AF:

0.224

AC:

7182

AN:

32102

American (AMR)

AF:

0.0230

AC:

880

AN:

38238

Ashkenazi Jewish (ASJ)

AF:

0.0341

AC:

865

AN:

25382

East Asian (EAS)

AF:

0.0326

AC:

1277

AN:

39138

South Asian (SAS)

AF:

0.0966

AC:

8095

AN:

83778

European-Finnish (FIN)

AF:

0.00843

AC:

445

AN:

52818

Middle Eastern (MID)

AF:

0.0454

AC:

258

AN:

5684

European-Non Finnish (NFE)

AF:

0.0189

AC:

20888

AN:

1102426

Other (OTH)

AF:

0.0398

AC:

2363

AN:

59386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

1959

3917

5876

7834

9793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

988

1976

2964

3952

4940

<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:

0.0769

AC:

11677

AN:

151894

Hom.:

1018

Cov.:

AF XY:

0.0763

AC XY:

5664

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.210

AC:

8682

AN:

41352

American (AMR)

AF:

0.0418

AC:

636

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.0338

AC:

117

AN:

3466

East Asian (EAS)

AF:

0.0374

AC:

193

AN:

5158

South Asian (SAS)

AF:

0.0970

AC:

467

AN:

4814

European-Finnish (FIN)

AF:

0.00717

AC:

AN:

10596

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0197

AC:

1336

AN:

67982

Other (OTH)

AF:

0.0714

AC:

150

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

460

919

1379

1838

2298

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0508

Hom.:

816

Bravo

AF:

0.0853

Asia WGS

AF:

0.0510

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.2

(source)

DANN

Benign

0.68

PhyloP100

1.1

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