chr10-133362754-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004092.4(ECHS1):c.*114C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,218,806 control chromosomes in the GnomAD database, including 1,163 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.054 ( 677 hom., cov: 33)
Exomes 𝑓: 0.0093 ( 486 hom. )
Consequence
ECHS1
NM_004092.4 3_prime_UTR
NM_004092.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0110
Genes affected
ECHS1 (HGNC:3151): (enoyl-CoA hydratase, short chain 1) The protein encoded by this gene functions in the second step of the mitochondrial fatty acid beta-oxidation pathway. It catalyzes the hydration of 2-trans-enoyl-coenzyme A (CoA) intermediates to L-3-hydroxyacyl-CoAs. The gene product is a member of the hydratase/isomerase superfamily. It localizes to the mitochondrial matrix. Transcript variants utilizing alternative transcription initiation sites have been described in the literature. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
Variant 10-133362754-G-A is Benign according to our data. Variant chr10-133362754-G-A is described in ClinVar as [Benign]. Clinvar id is 1258110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECHS1 | NM_004092.4 | c.*114C>T | 3_prime_UTR_variant | 8/8 | ENST00000368547.4 | NP_004083.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECHS1 | ENST00000368547.4 | c.*114C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_004092.4 | ENSP00000357535 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0538 AC: 8181AN: 152176Hom.: 673 Cov.: 33
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GnomAD4 exome AF: 0.00928 AC: 9899AN: 1066512Hom.: 486 Cov.: 14 AF XY: 0.00843 AC XY: 4604AN XY: 546430
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GnomAD4 genome AF: 0.0538 AC: 8201AN: 152294Hom.: 677 Cov.: 33 AF XY: 0.0522 AC XY: 3886AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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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