Genetic Variant NM_206836.3:c.674+272C>T (chr6-4125863-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_206836.3(ECI2):c.674+272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 550,548 control chromosomes in the GnomAD database, including 54,192 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 0.50 ( 21819 hom., cov: 33)

Exomes 𝑓: 0.39 ( 32373 hom. )

Consequence

ECI2
NM_206836.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

11 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECI2	NM_206836.3 link	c.674+272C>T		intron_variant	Intron 6 of 9	ENST00000380118.8	NP_996667.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECI2	ENST00000380118.8 link	c.674+272C>T		intron_variant	Intron 6 of 9	1	NM_206836.3	ENSP00000369461.3

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76596

AN:

152040

Hom.:

21776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.365

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.482

GnomAD2 exomes

AF:

0.406

AC:

40345

AN:

99462

AF XY:

0.395

show subpopulations

Gnomad AFR exome

AF:

0.802

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.343

Gnomad EAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.387

Gnomad NFE exome

AF:

0.396

Gnomad OTH exome

AF:

0.389

GnomAD4 exome

AF:

0.393

AC:

156578

AN:

398392

Hom.:

32373

Cov.:

AF XY:

0.385

AC XY:

84067

AN XY:

218604

show subpopulations

African (AFR)

AF:

0.789

AC:

9231

AN:

11698

American (AMR)

AF:

0.430

AC:

9779

AN:

22768

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

4609

AN:

13658

East Asian (EAS)

AF:

0.382

AC:

7749

AN:

20310

South Asian (SAS)

AF:

0.303

AC:

15965

AN:

52734

European-Finnish (FIN)

AF:

0.388

AC:

8152

AN:

21032

Middle Eastern (MID)

AF:

0.367

AC:

1201

AN:

3270

European-Non Finnish (NFE)

AF:

0.394

AC:

90900

AN:

230930

Other (OTH)

AF:

0.409

AC:

8992

AN:

21992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

4376

8752

13129

17505

21881

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.504

AC:

76698

AN:

152156

Hom.:

21819

Cov.:

AF XY:

0.498

AC XY:

37056

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.787

AC:

32690

AN:

41538

American (AMR)

AF:

0.453

AC:

6925

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1116

AN:

3470

East Asian (EAS)

AF:

0.364

AC:

1884

AN:

5170

South Asian (SAS)

AF:

0.303

AC:

1461

AN:

4822

European-Finnish (FIN)

AF:

0.403

AC:

4259

AN:

10558

Middle Eastern (MID)

AF:

0.395

AC:

116

AN:

294

European-Non Finnish (NFE)

AF:

0.396

AC:

26937

AN:

67982

Other (OTH)

AF:

0.479

AC:

1013

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1770

3539

5309

7078

8848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<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:

0.459

Hom.:

4009

Bravo

AF:

0.523

Asia WGS

AF:

0.352

AC:

1224

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.070

(source)

DANN

Benign

0.42

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