rs661404

Positions:

• chr6-4125863-G-A
• chr6-4125863-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.93).
• 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/exons	MANE	UniProt
ECI2	NM_206836.3	c.674+272C>T		intron_variant		ENST00000380118.8
TEX56P	NR_104463.3	n.2308G>A		non_coding_transcript_exon_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECI2	ENST00000380118.8	c.674+272C>T		intron_variant		1	NM_206836.3	P1
TEX56P	ENST00000643110.1	n.1147+3817G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76596 AN: 152040 Hom.: 21776 Cov.: 33

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

GnomAD3 exomes AF: 0.406 AC: 40345 AN: 99462 Hom.: 8774 AF XY: 0.395 AC XY: 21076 AN XY: 53332

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 SAS exome AF: 0.298

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.: 2 AF XY: 0.385 AC XY: 84067 AN XY: 218604

Gnomad4 AFR exome AF: 0.789

Gnomad4 AMR exome AF: 0.430

Gnomad4 ASJ exome AF: 0.337

Gnomad4 EAS exome AF: 0.382

Gnomad4 SAS exome AF: 0.303

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.409

GnomAD4 genome AF: 0.504 AC: 76698 AN: 152156 Hom.: 21819 Cov.: 33 AF XY: 0.498 AC XY: 37056 AN XY: 74372

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.479

Alfa AF: 0.452 Hom.: 3772

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
DANN	Benign	0.42

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: rs661404; hg19: chr6-4126097; COSMIC: COSV60986713; COSMIC: COSV60986713;