dbSNP rs3745816: 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

new If you want to explore the variant's impact on the transcript NM_012155.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012155.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EML2	NM_012155.4	MANE Select	c.*14G>A	3_prime_UTR	Exon 19 of 19	NP_036287.1	O95834-1
EML2	NM_001193268.3		c.*14G>A	3_prime_UTR	Exon 22 of 22	NP_001180197.1	O95834-3
EML2	NM_001352052.1		c.*14G>A	3_prime_UTR	Exon 22 of 22	NP_001338981.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EML2	ENST00000245925.8	TSL:1 MANE Select	c.*14G>A	3_prime_UTR	Exon 19 of 19	ENSP00000245925.3	O95834-1
EML2	ENST00000589876.5	TSL:1	c.1825-2143G>A	intron	N/A	ENSP00000464789.1	K7EIK7
EML2	ENST00000587152.6	TSL:2	c.*14G>A	3_prime_UTR	Exon 22 of 22	ENSP00000468312.1	O95834-3

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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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