5-79028529-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013391.3(DMGDH):āc.1936T>Cā(p.Ser646Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,613,646 control chromosomes in the GnomAD database, including 69,821 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013391.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMGDH | NM_013391.3 | c.1936T>C | p.Ser646Pro | missense_variant | 12/16 | ENST00000255189.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMGDH | ENST00000255189.8 | c.1936T>C | p.Ser646Pro | missense_variant | 12/16 | 1 | NM_013391.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.326 AC: 49564AN: 151820Hom.: 8771 Cov.: 31
GnomAD3 exomes AF: 0.274 AC: 68746AN: 251270Hom.: 10276 AF XY: 0.277 AC XY: 37636AN XY: 135786
GnomAD4 exome AF: 0.284 AC: 414880AN: 1461706Hom.: 61041 Cov.: 36 AF XY: 0.285 AC XY: 206944AN XY: 727166
GnomAD4 genome AF: 0.326 AC: 49603AN: 151940Hom.: 8780 Cov.: 31 AF XY: 0.324 AC XY: 24056AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2015 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at