6-4118555-G-A

Variant names:

• chr6-4118555-G-A
• rs584585
• NM_206836.3:c.885+631C>T

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+631C>T 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 152,194 control chromosomes in the GnomAD database, including 6,812 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 (6812 hom., cov: 33)
  • Exomes 𝑓: 0.29 (0 hom.)
• Consequence: ECI2 NM_206836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 10 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 = 0.35 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+631C>T		intron	N/A	NP_996667.2
	ECI2	NM_001166010.2		c.795+631C>T		intron	N/A	NP_001159482.1
	ECI2	NM_006117.3		c.795+631C>T		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+631C>T		intron	N/A	ENSP00000369461.3
	ECI2	ENST00000361538.6	TSL:1	c.795+631C>T		intron	N/A	ENSP00000354737.2
	ECI2	ENST00000380125.6	TSL:1	c.795+631C>T		intron	N/A	ENSP00000369468.2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44991 AN: 152048 Hom.: 6809 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.364

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: 0.286 AC: 8 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.273 AC XY: 6 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.269 AC: 7 AN: 26

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.296 AC: 45018 AN: 152166 Hom.: 6812 Cov.: 33 AF XY: 0.292 AC XY: 21762 AN XY: 74412

African (AFR) AF: 0.265 AC: 10990 AN: 41520

American (AMR) AF: 0.357 AC: 5449 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1881 AN: 5176

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2779 AN: 10598

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

European-Non Finnish (NFE) AF: 0.307 AC: 20848 AN: 67980

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

Alfa AF: 0.289 Hom.: 1205

Bravo AF: 0.305

Asia WGS AF: 0.293 AC: 1020 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	0.15
DANN	Benign	0.70
PhyloP100		-0.57
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: rs584585; hg19: chr6-4118789;