6-4118817-C-T

Variant names:

• chr6-4118817-C-T
• rs659025
• NM_206836.3:c.885+369G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206836.3(ECI2):​c.885+369G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 171,116 control chromosomes in the GnomAD database, including 7,734 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 (6815 hom., cov: 33)
  • Exomes 𝑓: 0.30 (919 hom.)
• Consequence: ECI2 NM_206836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 8 publications found

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]

TEX56P (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206836.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECI2	NM_206836.3	MANE Select	c.885+369G>A		intron	N/A	NP_996667.2
	ECI2	NM_001166010.2		c.795+369G>A		intron	N/A	NP_001159482.1
	ECI2	NM_006117.3		c.795+369G>A		intron	N/A	NP_006108.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECI2	ENST00000380118.8	TSL:1 MANE Select	c.885+369G>A		intron	N/A	ENSP00000369461.3
	ECI2	ENST00000361538.6	TSL:1	c.795+369G>A		intron	N/A	ENSP00000354737.2
	ECI2	ENST00000380125.6	TSL:1	c.795+369G>A		intron	N/A	ENSP00000369468.2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44985 AN: 152038 Hom.: 6812 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.324

GnomAD4 exome AF: 0.298 AC: 5649 AN: 18960 Hom.: 919 Cov.: 0 AF XY: 0.289 AC XY: 2977 AN XY: 10300

African (AFR) AF: 0.274 AC: 92 AN: 336

American (AMR) AF: 0.366 AC: 779 AN: 2126

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 120 AN: 452

East Asian (EAS) AF: 0.399 AC: 485 AN: 1216

South Asian (SAS) AF: 0.229 AC: 438 AN: 1916

European-Finnish (FIN) AF: 0.246 AC: 128 AN: 520

Middle Eastern (MID) AF: 0.293 AC: 17 AN: 58

European-Non Finnish (NFE) AF: 0.291 AC: 3338 AN: 11482

Other (OTH) AF: 0.295 AC: 252 AN: 854

GnomAD4 genome AF: 0.296 AC: 45012 AN: 152156 Hom.: 6815 Cov.: 33 AF XY: 0.292 AC XY: 21751 AN XY: 74392

African (AFR) AF: 0.265 AC: 10977 AN: 41494

American (AMR) AF: 0.357 AC: 5459 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1869 AN: 5158

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2776 AN: 10596

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20859 AN: 68006

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.287 Hom.: 4878

Bravo AF: 0.305

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.76
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs659025; hg19: chr6-4119051;