6-4125863-G-C

Variant names:

• chr6-4125863-G-C
• rs661404
• NM_206836.3:c.674+272C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_206836.3(ECI2):​c.674+272C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ECI2 NM_206836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 11 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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.674+272C>G		intron	N/A	NP_996667.2
	TEX56P	NR_104463.3		n.2308G>C		non_coding_transcript_exon	Exon 6 of 8
	TEX56P	NR_104464.3		n.1654G>C		non_coding_transcript_exon	Exon 4 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECI2	ENST00000380118.8	TSL:1 MANE Select	c.674+272C>G		intron	N/A	ENSP00000369461.3
	ECI2	ENST00000361538.6	TSL:1	c.584+272C>G		intron	N/A	ENSP00000354737.2
	ECI2	ENST00000380125.6	TSL:1	c.584+272C>G		intron	N/A	ENSP00000369468.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 399360 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 219180

African (AFR) AF: 0.00 AC: 0 AN: 11714

American (AMR) AF: 0.00 AC: 0 AN: 22836

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13710

East Asian (EAS) AF: 0.00 AC: 0 AN: 20394

South Asian (SAS) AF: 0.00 AC: 0 AN: 52814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21090

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3278

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 231476

Other (OTH) AF: 0.00 AC: 0 AN: 22048

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.057
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs661404; hg19: chr6-4126097;