5-79024325-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_013391.3(DMGDH):c.2196C>T(p.Asn732=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000105 in 1,613,382 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000097 ( 1 hom. )
Consequence
DMGDH
NM_013391.3 synonymous
NM_013391.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.49
Genes affected
DMGDH (HGNC:24475): (dimethylglycine dehydrogenase) This gene encodes an enzyme involved in the catabolism of choline, catalyzing the oxidative demethylation of dimethylglycine to form sarcosine. The enzyme is found as a monomer in the mitochondrial matrix, and uses flavin adenine dinucleotide and folate as cofactors. Mutation in this gene causes dimethylglycine dehydrogenase deficiency, characterized by a fishlike body odor, chronic muscle fatigue, and elevated levels of the muscle form of creatine kinase in serum. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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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
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 5-79024325-G-A is Benign according to our data. Variant chr5-79024325-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 510489.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMGDH | NM_013391.3 | c.2196C>T | p.Asn732= | synonymous_variant | 14/16 | ENST00000255189.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMGDH | ENST00000255189.8 | c.2196C>T | p.Asn732= | synonymous_variant | 14/16 | 1 | NM_013391.3 | P1 | |
DMGDH | ENST00000523732.1 | c.1713C>T | p.Asn571= | synonymous_variant | 11/12 | 1 | |||
DMGDH | ENST00000517853.5 | c.*958C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 | ||||
DMGDH | ENST00000518477.5 | c.*1430C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152190Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000163 AC: 41AN: 250898Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135608
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GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461074Hom.: 1 Cov.: 30 AF XY: 0.000105 AC XY: 76AN XY: 726874
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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 | Jul 05, 2017 | 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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Name
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BayesDel_noAF
Benign
Cadd
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Dann
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at