rs200278015
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM2PP3BP4_ModerateBP6
The NM_012213.3(MLYCD):c.1328G>C(p.Gly443Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,613,784 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G443G) has been classified as Likely benign.
Frequency
Consequence
NM_012213.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLYCD | NM_012213.3 | c.1328G>C | p.Gly443Ala | missense_variant | 5/5 | ENST00000262430.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.1328G>C | p.Gly443Ala | missense_variant | 5/5 | 1 | NM_012213.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000418 AC: 104AN: 248968Hom.: 0 AF XY: 0.000429 AC XY: 58AN XY: 135252
GnomAD4 exome AF: 0.000243 AC: 355AN: 1461578Hom.: 0 Cov.: 30 AF XY: 0.000272 AC XY: 198AN XY: 727104
GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74366
ClinVar
Submissions by phenotype
Deficiency of malonyl-CoA decarboxylase Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Mar 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at