rs7744628

Positions:

• chr6-4119762-T-C
• chr6-4119762-T-G

Variant summary

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

The NM_206836.3(ECI2):​c.796-487A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,994 control chromosomes in the GnomAD database, including 7,171 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 (7171 hom., cov: 32)
• Consequence: ECI2 NM_206836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECI2	NM_206836.3	c.796-487A>G		intron_variant		ENST00000380118.8
TEX56P	NR_104463.3	n.1307-2187T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECI2	ENST00000380118.8	c.796-487A>G		intron_variant		1	NM_206836.3	P1
TEX56P	ENST00000642280.1	n.616-2187T>C		intron_variant, non_coding_transcript_variant
TEX56P	ENST00000643110.1	n.1050-2187T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46236 AN: 151874 Hom.: 7168 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.304 AC: 46264 AN: 151994 Hom.: 7171 Cov.: 32 AF XY: 0.301 AC XY: 22343 AN XY: 74276

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.332

Alfa AF: 0.214 Hom.: 612

Bravo AF: 0.315

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.47

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: rs7744628; hg19: chr6-4119996;