16-83899588-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_012213.3(MLYCD):c.444C>T(p.Asp148Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 1,589,408 control chromosomes in the GnomAD database, including 435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_012213.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.444C>T | p.Asp148Asp | synonymous_variant | Exon 1 of 5 | 1 | NM_012213.3 | ENSP00000262430.4 | ||
ENSG00000288849 | ENST00000689373.1 | n.1202-7399C>T | intron_variant | Intron 5 of 8 | ||||||
ENSG00000288849 | ENST00000692462.1 | n.1170-7399C>T | intron_variant | Intron 5 of 8 |
Frequencies
GnomAD3 genomes AF: 0.0331 AC: 5043AN: 152198Hom.: 196 Cov.: 33
GnomAD3 exomes AF: 0.0132 AC: 2678AN: 202962Hom.: 62 AF XY: 0.0121 AC XY: 1368AN XY: 113526
GnomAD4 exome AF: 0.0104 AC: 14934AN: 1437094Hom.: 237 Cov.: 30 AF XY: 0.0100 AC XY: 7161AN XY: 714780
GnomAD4 genome AF: 0.0333 AC: 5070AN: 152314Hom.: 198 Cov.: 33 AF XY: 0.0319 AC XY: 2373AN XY: 74478
ClinVar
Submissions by phenotype
Deficiency of malonyl-CoA decarboxylase Benign:2
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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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:2
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. -
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at