16-83899115-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012213.3(MLYCD):c.-30G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000319 in 1,097,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000087 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
MLYCD
NM_012213.3 5_prime_UTR
NM_012213.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0780
Genes affected
MLYCD (HGNC:7150): (malonyl-CoA decarboxylase) The product of this gene catalyzes the breakdown of malonyl-CoA to acetyl-CoA and carbon dioxide. Malonyl-CoA is an intermediate in fatty acid biosynthesis, and also inhibits the transport of fatty acyl CoAs into mitochondria. Consequently, the encoded protein acts to increase the rate of fatty acid oxidation. It is found in mitochondria, peroxisomes, and the cytoplasm. Mutations in this gene result in malonyl-CoA decarboyxlase deficiency. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
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Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 16-83899115-G-C is Benign according to our data. Variant chr16-83899115-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 389744.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLYCD | NM_012213.3 | c.-30G>C | 5_prime_UTR_variant | 1/5 | ENST00000262430.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.-30G>C | 5_prime_UTR_variant | 1/5 | 1 | NM_012213.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000934 AC: 14AN: 149926Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000232 AC: 22AN: 947094Hom.: 0 Cov.: 28 AF XY: 0.0000403 AC XY: 18AN XY: 446804
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GnomAD4 genome ? AF: 0.0000866 AC: 13AN: 150034Hom.: 0 Cov.: 33 AF XY: 0.0000956 AC XY: 7AN XY: 73234
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 07, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at