1-75724531-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 ENST00000541113.6(ACADM):c.-257G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 411,780 control chromosomes in the GnomAD database, including 16,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.27 ( 5739 hom., cov: 31)
Exomes 𝑓: 0.28 ( 10987 hom. )
Consequence
ACADM
ENST00000541113.6 5_prime_UTR
ENST00000541113.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.23
Genes affected
ACADM (HGNC:89): (acyl-CoA dehydrogenase medium chain) This gene encodes the medium-chain specific (C4 to C12 straight chain) acyl-Coenzyme A dehydrogenase. The homotetramer enzyme catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Defects in this gene cause medium-chain acyl-CoA dehydrogenase deficiency, a disease characterized by hepatic dysfunction, fasting hypoglycemia, and encephalopathy, which can result in infantile death. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [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=-0.88).
BP6
Variant 1-75724531-G-A is Benign according to our data. Variant chr1-75724531-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 298063.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACADM | ENST00000541113.6 | c.-257G>A | 5_prime_UTR_variant | 1/11 | 1 | ||||
ACADM | ENST00000680805.1 | c.-257G>A | 5_prime_UTR_variant | 1/11 | |||||
ACADM | ENST00000680964.1 | c.-257G>A | 5_prime_UTR_variant | 1/12 |
Frequencies
GnomAD3 genomes AF: 0.269 AC: 40880AN: 151966Hom.: 5738 Cov.: 31
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GnomAD4 exome AF: 0.276 AC: 71619AN: 259696Hom.: 10987 Cov.: 2 AF XY: 0.276 AC XY: 37174AN XY: 134446
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GnomAD4 genome AF: 0.269 AC: 40878AN: 152084Hom.: 5739 Cov.: 31 AF XY: 0.268 AC XY: 19924AN XY: 74310
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Medium-chain acyl-coenzyme A dehydrogenase deficiency Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 06, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at