Genetic Variant ECI2:c.675-337T>C (chr6-4125707-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.675-337T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 417,878 control chromosomes in the GnomAD database, including 20,151 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 0.32 ( 7970 hom., cov: 33)

Exomes 𝑓: 0.30 ( 12181 hom. )

Consequence

ECI2
NM_206836.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.599

Publications

10 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=-0.95).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECI2	NM_206836.3 link	c.675-337T>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.675-337T>C		intron_variant	Intron 6 of 9	1	NM_206836.3	ENSP00000369461.3		O75521-1

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48766

AN:

152018

Hom.:

7963

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.342

GnomAD4 exome

AF:

0.298

AC:

79175

AN:

265742

Hom.:

12181

Cov.:

AF XY:

0.294

AC XY:

41969

AN XY:

142560

show subpopulations

African (AFR)

AF:

0.351

AC:

2826

AN:

8060

American (AMR)

AF:

0.360

AC:

3940

AN:

10946

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

1950

AN:

7612

East Asian (EAS)

AF:

0.372

AC:

4898

AN:

13170

South Asian (SAS)

AF:

0.249

AC:

9668

AN:

38848

European-Finnish (FIN)

AF:

0.251

AC:

3303

AN:

13148

Middle Eastern (MID)

AF:

0.303

AC:

751

AN:

2476

European-Non Finnish (NFE)

AF:

0.303

AC:

47461

AN:

156822

Other (OTH)

AF:

0.299

AC:

4378

AN:

14660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2620

5239

7859

10478

13098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.321

AC:

48805

AN:

152136

Hom.:

7970

Cov.:

AF XY:

0.316

AC XY:

23518

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.351

AC:

14570

AN:

41510

American (AMR)

AF:

0.366

AC:

5603

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3468

East Asian (EAS)

AF:

0.363

AC:

1872

AN:

5156

South Asian (SAS)

AF:

0.247

AC:

1190

AN:

4822

European-Finnish (FIN)

AF:

0.261

AC:

2765

AN:

10592

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20877

AN:

67982

Other (OTH)

AF:

0.341

AC:

720

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1719

3438

5156

6875

8594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.309

Hom.:

3896

Bravo

AF:

0.334

Asia WGS

AF:

0.297

AC:

1034

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.1

(source)

DANN

Benign

0.52

PhyloP100

0.60

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