chr15-89319110-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002693.3(POLG):c.3105-11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 1,613,784 control chromosomes in the GnomAD database, including 119,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002693.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.332 AC: 50436AN: 151960Hom.: 9208 Cov.: 33
GnomAD3 exomes AF: 0.377 AC: 94663AN: 251428Hom.: 18606 AF XY: 0.383 AC XY: 52018AN XY: 135890
GnomAD4 exome AF: 0.385 AC: 562801AN: 1461706Hom.: 110095 Cov.: 45 AF XY: 0.386 AC XY: 280932AN XY: 727164
GnomAD4 genome AF: 0.332 AC: 50444AN: 152078Hom.: 9212 Cov.: 33 AF XY: 0.340 AC XY: 25269AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:6
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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This variant is classified as Benign based on local population frequency. This variant was detected in 52% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 48. Only high quality variants are reported. -
Progressive sclerosing poliodystrophy Benign:3
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The NM_002693.2:c.3105-11T>C (NP_002684.1:p.=) [GRCH38: NC_000015.10:g.89319110A>G] variant in POLG gene is interpretated to be a Benign based on ACMG guidelines (PMID: 25741868). This variant meets the following evidence codes reported in the ACMG-guideline. BA1:Minor allele frequency is too high for the Mitochondrial DNA depletion syndrome 4A (Alpers type). BS1:The minor allele frequency of this allele is high for Mitochondrial DNA depletion syndrome 4A (Alpers type). BS2:Observation of the variant in controls is inconsistent with penetrance of Mitochondrial DNA depletion syndrome 4A (Alpers type). Based on the evidence criteria codes applied, the variant is suggested to be Benign. -
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 Benign:1
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Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 Benign:1
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POLG-Related Spectrum Disorders Benign:1
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Fanconi anemia Benign:1
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Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis Benign:1
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not provided Benign:1
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Mitochondrial DNA depletion syndrome 4b Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at