chr16-83899153-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_012213.3(MLYCD):c.9C>T(p.Gly3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000523 in 1,147,260 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 (★). Synonymous variant affecting the same amino acid position (i.e. G3G) has been classified as Likely benign.
Frequency
Consequence
NM_012213.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLYCD | NM_012213.3 | c.9C>T | p.Gly3= | synonymous_variant | 1/5 | ENST00000262430.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.9C>T | p.Gly3= | synonymous_variant | 1/5 | 1 | NM_012213.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000134 AC: 2AN: 149718Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000401 AC: 4AN: 997434Hom.: 0 Cov.: 28 AF XY: 0.00000839 AC XY: 4AN XY: 476486
GnomAD4 genome ? AF: 0.0000133 AC: 2AN: 149826Hom.: 0 Cov.: 33 AF XY: 0.0000273 AC XY: 2AN XY: 73130
ClinVar
Submissions by phenotype
Deficiency of malonyl-CoA decarboxylase Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at