dbSNP rs1961245: EML6:c.1933-61G>A (chr2-54866705-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001039753.4(EML6):c.1933-61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 845,580 control chromosomes in the GnomAD database, including 73,407 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 0.45 ( 16240 hom., cov: 32)

Exomes 𝑓: 0.40 ( 57167 hom. )

Consequence

EML6
NM_001039753.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

Publications

8 publications found

Variant links:

Genes affected

EML6 (HGNC:35412): (EMAP like 6) Predicted to enable microtubule binding activity. Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

EML6 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EML6	NM_001039753.4 link	c.1933-61G>A		intron_variant	Intron 13 of 41	ENST00000356458.8	NP_001034842.2	Q6ZMW3-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
EML6	ENST00000356458.8 link	c.1933-61G>A	intron_variant	Intron 13 of 41	5	NM_001039753.4	ENSP00000348842.6	Q6ZMW3-1
EML6	ENST00000493997.1 link	n.281-61G>A	intron_variant	Intron 3 of 5	5
EML6	ENST00000673912.1 link	n.1933-61G>A	intron_variant	Intron 13 of 42			ENSP00000501234.1	A0A669KBD4

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68112

AN:

151922

Hom.:

16222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.547

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.440

GnomAD4 exome

AF:

0.396

AC:

274347

AN:

693540

Hom.:

57167

AF XY:

0.402

AC XY:

144208

AN XY:

358838

show subpopulations

African (AFR)

AF:

0.614

AC:

10506

AN:

17102

American (AMR)

AF:

0.413

AC:

9921

AN:

24046

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

6983

AN:

17548

East Asian (EAS)

AF:

0.549

AC:

17545

AN:

31938

South Asian (SAS)

AF:

0.559

AC:

27828

AN:

49800

European-Finnish (FIN)

AF:

0.423

AC:

19112

AN:

45180

Middle Eastern (MID)

AF:

0.458

AC:

1896

AN:

4142

European-Non Finnish (NFE)

AF:

0.355

AC:

166927

AN:

470590

Other (OTH)

AF:

0.411

AC:

13629

AN:

33194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

7753

15506

23260

31013

38766

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3796

7592

11388

15184

18980

<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:

0.448

AC:

68181

AN:

152040

Hom.:

16240

Cov.:

AF XY:

0.453

AC XY:

33705

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.597

AC:

24751

AN:

41468

American (AMR)

AF:

0.414

AC:

6333

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1404

AN:

3470

East Asian (EAS)

AF:

0.546

AC:

2824

AN:

5172

South Asian (SAS)

AF:

0.566

AC:

2728

AN:

4822

European-Finnish (FIN)

AF:

0.443

AC:

4672

AN:

10554

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.354

AC:

24022

AN:

67950

Other (OTH)

AF:

0.440

AC:

931

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1856

3713

5569

7426

9282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.390

Hom.:

8952

Bravo

AF:

0.451

Asia WGS

AF:

0.554

AC:

1925

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.16

(source)

DANN

Benign

0.19

PhyloP100

-1.0

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