chr6-4118555-G-A

Position:

• chr6-4118555-G-A

Variant summary

Our verdict is Benign. Variant got -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

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:21620): (testis expressed 56, pseudogene)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECI2	NM_206836.3	c.885+631C>T		intron_variant		ENST00000380118.8
TEX56P	NR_104463.3	n.1306+2892G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECI2	ENST00000380118.8	c.885+631C>T		intron_variant		1	NM_206836.3	P1
TEX56P	ENST00000642280.1	n.615+2892G>A		intron_variant, non_coding_transcript_variant
TEX56P	ENST00000643110.1	n.1050-3394G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.269

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

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.323

Alfa AF: 0.289 Hom.: 1176

Bravo AF: 0.305

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.70

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

LitVar

Other links and lift over

dbSNP: rs584585; hg19: chr6-4118789;