rs584585
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_206836.3 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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: 44991AN: 152048Hom.: 6809 Cov.: 33
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33
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GnomAD4 exome AF: 0.286 AC: 8AN: 28Hom.: 0 Cov.: 0 AF XY: 0.273 AC XY: 6AN XY: 22
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GnomAD4 genome ? AF: 0.296 AC: 45018AN: 152166Hom.: 6812 Cov.: 33 AF XY: 0.292 AC XY: 21762AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at