Genetic Variant NM_206836.3: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:

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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

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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