Genetic Variant ECI2:c.675-51T>C (chr6-4125421-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_206836.3(ECI2):c.675-51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,608,078 control chromosomes in the GnomAD database, including 78,978 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 0.30 ( 7083 hom., cov: 33)

Exomes 𝑓: 0.31 ( 71895 hom. )

Consequence

ECI2
NM_206836.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

18 publications found

Variant links:

Genes affected

ECI2 (HGNC:14601): (enoyl-CoA delta isomerase 2) This gene encodes a member of the hydratase/isomerase superfamily. The protein encoded is a key mitochondrial enzyme involved in beta-oxidation of unsaturated fatty acids. It catalyzes the transformation of 3-cis and 3-trans-enoyl-CoA esters arising during the stepwise degradation of cis-, mono-, and polyunsaturated fatty acids to the 2-trans-enoyl-CoA intermediates. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2011]

ECI2 links:

TEX56P (HGNC:):

TEX56P links:

TEX56P (HGNC:21620): (testis expressed 56, pseudogene)

TEX56P 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECI2	NM_206836.3 link	c.675-51T>C		intron_variant	Intron 6 of 9	ENST00000380118.8	NP_996667.2	O75521-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECI2	ENST00000380118.8 link	c.675-51T>C		intron_variant	Intron 6 of 9	1	NM_206836.3	ENSP00000369461.3		O75521-1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45945

AN:

152070

Hom.:

7079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.328

GnomAD2 exomes

AF:

0.303

AC:

74433

AN:

245752

AF XY:

0.300

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.367

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.372

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.302

Gnomad OTH exome

AF:

0.306

GnomAD4 exome

AF:

0.313

AC:

455456

AN:

1455890

Hom.:

71895

Cov.:

AF XY:

0.310

AC XY:

224759

AN XY:

724208

show subpopulations

African (AFR)

AF:

0.284

AC:

9488

AN:

33430

American (AMR)

AF:

0.368

AC:

16422

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

6822

AN:

25978

East Asian (EAS)

AF:

0.386

AC:

15314

AN:

39632

South Asian (SAS)

AF:

0.248

AC:

21289

AN:

85938

European-Finnish (FIN)

AF:

0.255

AC:

12832

AN:

50342

Middle Eastern (MID)

AF:

0.302

AC:

1739

AN:

5760

European-Non Finnish (NFE)

AF:

0.318

AC:

352931

AN:

1109926

Other (OTH)

AF:

0.309

AC:

18619

AN:

60244

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

14422

28844

43265

57687

72109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11756

23512

35268

47024

58780

<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:

0.302

AC:

45973

AN:

152188

Hom.:

7083

Cov.:

AF XY:

0.298

AC XY:

22209

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.286

AC:

11860

AN:

41500

American (AMR)

AF:

0.359

AC:

5494

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

870

AN:

3470

East Asian (EAS)

AF:

0.363

AC:

1882

AN:

5186

South Asian (SAS)

AF:

0.246

AC:

1188

AN:

4828

European-Finnish (FIN)

AF:

0.261

AC:

2769

AN:

10592

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20882

AN:

68000

Other (OTH)

AF:

0.327

AC:

690

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1679

3357

5036

6714

8393

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.308

Hom.:

21089

Bravo

AF:

0.312

Asia WGS

AF:

0.294

AC:

1022

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.65

(source)

DANN

Benign

0.57

PhyloP100

-1.3

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over