6-4121099-C-T

Variant names:

• chr6-4121099-C-T
• rs9503922
• NM_206836.3:c.796-1824G>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.796-1824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,132 control chromosomes in the GnomAD database, including 4,257 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 0.23 (4257 hom., cov: 32)
• Consequence: ECI2 NM_206836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECI2	NM_206836.3	c.796-1824G>A		intron_variant	Intron 7 of 9	ENST00000380118.8	NP_996667.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECI2	ENST00000380118.8	c.796-1824G>A		intron_variant	Intron 7 of 9	1	NM_206836.3	ENSP00000369461.3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34970 AN: 152016 Hom.: 4258 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.230 AC: 34986 AN: 152132 Hom.: 4257 Cov.: 32 AF XY: 0.223 AC XY: 16565 AN XY: 74386

African (AFR) AF: 0.234 AC: 9723 AN: 41480

American (AMR) AF: 0.203 AC: 3109 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.0202 AC: 105 AN: 5186

South Asian (SAS) AF: 0.131 AC: 633 AN: 4826

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10578

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17469 AN: 67982

Other (OTH) AF: 0.247 AC: 522 AN: 2114

Alfa AF: 0.148 Hom.: 289

Bravo AF: 0.231

Asia WGS AF: 0.0970 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		-0.33
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: rs9503922; hg19: chr6-4121333;