rs200257554
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_002693.3(POLG):c.2021G>A(p.Gly674Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000299 in 1,613,856 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002693.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000605 AC: 152AN: 251084Hom.: 0 AF XY: 0.000685 AC XY: 93AN XY: 135718
GnomAD4 exome AF: 0.000313 AC: 457AN: 1461624Hom.: 3 Cov.: 32 AF XY: 0.000396 AC XY: 288AN XY: 727108
GnomAD4 genome AF: 0.000171 AC: 26AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74366
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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This variant is associated with the following publications: (PMID: 26557169) -
Progressive sclerosing poliodystrophy Benign:2
The NM_002693.2:c.2021G>A (NP_002684.1:p.Gly674Asp) [GRCH38: NC_000015.10:g.89324156C>T] variant in POLG gene is interpretated to be a Likely Benign based on ACMG guidelines (PMID: 25741868). This variant meets the following evidence codes reported in the ACMG-guideline. BS1:The minor allele frequency of this allele is high for Mitochondrial DNA depletion syndrome 4A (Alpers type). BP4:Computational evidence/predictors indicate no impact on the POLG structure, function, or protein-protein interaction. BP7:The variant is silent with non predicted splice impact. Based on the evidence criteria codes applied, the variant is suggested to be Likely Benign. -
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POLG-Related Spectrum Disorders Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Inborn genetic diseases Uncertain:1
The p.G674D variant (also known as c.2021G>A), located in coding exon 10 of the POLG gene, results from a G to A substitution at nucleotide position 2021. The glycine at codon 674 is replaced by aspartic acid, an amino acid with similar properties. This alteration was detected in an individual with paroxysmal exertion induced dystonia (PED) and early onset exertion induced dystonia in conjunction with a second POLG alteration of unknown significance (c.3644-­27T>G). The p.G674D alteration was also detected in the individual's father. Both the proband and his father also carried the SURF1 c.237G>T alteration which authors considered to be pathogenic; therefore, it is unknown which alteration(s) is causative (Chandra SR et al. J Pediatr Neurosci;10:254-7). This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Progressive sclerosing poliodystrophy;C1834846:Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;C1843851:Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;C3150914:Mitochondrial DNA depletion syndrome 4b;C4225153:Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 Uncertain:1
POLG NM_002693 exon 11 p.Gly674Asp (c.2021G>A): This variant has not been reported in the literature but is present in 0.1% (55/30782) of South Asian individuals in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs200257554). This variant is present in ClinVar (Variation ID:206462). This variant Aspartic Acid (Asp) is present in >5 species (including mammals) and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
not specified Benign:1
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POLG-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at