owencqueen/cgbench_data huggingface dataset:
Gene: POLG (HGNC:9179)
Evidence Code: PS2 — Original ACMG Summary
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity.
Gene: POLG (HGNC:9179)
Evidence Code: PS2 — Strong
De novo in a patient with the disease and no family history
Gene: POLG (HGNC:9179)
Evidence Code: PS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.
Gene: POLG (HGNC:9179)
Evidence Code: PS4 — Original ACMG Summary
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.
Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance.
Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.
Gene: POLG (HGNC:9179)
Evidence Code: PS4 — Strong
Rarely, pathogenic variants cause disease in an AD manner. For these variants only, presence in: 2 unrelated probands will be considered supporting evidence, 4 unrelated probands will be considered moderate evidence, 16 unrelated probands will be strong evidence.




Note: This will only be utilized when there is segregation evidence supporting autosomal dominant inheritance
Gene: POLG (HGNC:9179)
Evidence Code: PM1 — Original ACMG Summary
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
Gene: POLG (HGNC:9179)
Evidence Code: PM2 — Original ACMG Summary
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Caveat: Population data for indels may be poorly called by next generation sequencing.
Gene: POLG (HGNC:9179)
Evidence Code: PM2 — Moderate
<0.0005 (<0.05% )
Gene: POLG (HGNC:9179)
Evidence Code: PM3 — Original ACMG Summary
For recessive disorders, detected in trans with a pathogenic variant
Note: This requires testing of parents (or offspring) to determine phase.
Gene: POLG (HGNC:9179)
Evidence Code: PM3 — Moderate
Use per SVI guidance.
Note: T251I and P587L are almost always in cis
Gene: POLG (HGNC:9179)
Evidence Code: PM4 — Original ACMG Summary
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
Gene: POLG (HGNC:9179)
Evidence Code: PM4 — Moderate
Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Gene: POLG (HGNC:9179)
Evidence Code: PM5 — Original ACMG Summary
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Example: Arg156His is pathogenic; now you observe Arg156Cys.
Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Gene: POLG (HGNC:9179)
Evidence Code: PM5 — Moderate
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
Gene: POLG (HGNC:9179)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: POLG (HGNC:9179)
Evidence Code: PM6 — Strong
De novo in a patient with the disease and no family history
Gene: POLG (HGNC:9179)
Evidence Code: PM6 — Moderate
Assumed de novo, but without confirmation of paternity and maternity
Gene: POLG (HGNC:9179)
Evidence Code: PP1 — Original ACMG Summary
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
Note: May be used as stronger evidence with increasing segregation data.
Gene: POLG (HGNC:9179)
Evidence Code: PP1 — Supporting
Further define “affected” as an individual in whom there is objective evidence of manifestations consistent with POLG-related disorders spectrum: Alpers-Huttenlocher syndrome (AHS), childhood myocerebrohepatopathy spectrum (MCHS), myoclonic epilepsy myopathy sensory ataxia (MEMSA), ataxia neuropathy spectrum (ANS), and/or progressive external ophthalmoplegia (PEO)
Gene: POLG (HGNC:9179)
Evidence Code: PP2 — Original ACMG Summary
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Gene: POLG (HGNC:9179)
Evidence Code: PP3 — Original ACMG Summary
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant.
Gene: POLG (HGNC:9179)
Evidence Code: PP3 — Supporting
Agree to utilize REVEL, with thresholds of >0.75 and <0.15 for PP3 and BP4, respectively




Will also utilize POLG pathogenicity prediction server if/when live again (PMID: 28480171); both tools (REVEL and server) will have to be in agreement to score
Gene: POLG (HGNC:9179)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: POLG (HGNC:9179)
Evidence Code: PP4 — Moderate
Mitochondrial DNA depletion showing ≤ 20% of controls, OR 


Multiple mitochondrial DNA deletions (NOTE:depletion and/or deletion analysis must be performed in muscle and/or liver; other tissues such as blood, fibroblast, and buccal are not acceptable; Must be performed in child, as defined as <18 years old) 
Note: For both scenarios 1 and 2, will only apply if other mtDNA maintenance disorders have been excluded (exome sequencing or comprehensive panel-based testing)
Gene: POLG (HGNC:9179)
Evidence Code: PP4 — Supporting
Mitochondrial DNA depletion showing 20-50% of controls in children (< 18 years of age), AND/OR 


COX negative fibers in muscle in children and/or adults
Note: Will only apply if other mtDNA maintenance disorders have been excluded (exome sequencing or comprehensive panel-based testing)
Gene: POLG (HGNC:9179)
Evidence Code: PP5 — Original ACMG Summary
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: POLG (HGNC:9179)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Gene: POLG (HGNC:9179)
Evidence Code: BA1 — Stand Alone
0.01 (>1%)
Gene: POLG (HGNC:9179)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: POLG (HGNC:9179)
Evidence Code: BS1 — Strong
0.005 (>0.5% - AR)
Gene: POLG (HGNC:9179)
Evidence Code: BS2 — Original ACMG Summary
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Gene: POLG (HGNC:9179)
Evidence Code: BS2 — Strong
Observed in a healthy adult individual in the homozygous state AND/OR Normal mtDNA content (1. Must be performed in muscle and/or liver; blood, fibroblast, and buccal not acceptable; 2. Must be performed in children only - defined as <18 years old; 3. A normal level is defined as >50%.)
Gene: POLG (HGNC:9179)
Evidence Code: BS2 — Supporting
Lack of COX negative fibers in muscle (children and adults)
Gene: POLG (HGNC:9179)
Evidence Code: BS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Gene: POLG (HGNC:9179)
Evidence Code: BS4 — Original ACMG Summary
Lack of segregation in affected members of a family.
Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation.
Gene: POLG (HGNC:9179)
Evidence Code: BS4 — Strong
Lack of segregation in affected and/or treated members of a family.
Gene: POLG (HGNC:9179)
Evidence Code: BP1 — Original ACMG Summary
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Gene: POLG (HGNC:9179)
Evidence Code: BP2 — Original ACMG Summary
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Gene: POLG (HGNC:9179)
Evidence Code: BP2 — Supporting
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern
Gene: POLG (HGNC:9179)
Evidence Code: BP3 — Original ACMG Summary
In frame-deletions/insertions in a repetitive region without a known function.
Gene: POLG (HGNC:9179)
Evidence Code: BP3 — Supporting
In-frame deletions/insertions in a repetitive region without a known function
Gene: POLG (HGNC:9179)
Evidence Code: BP4 — Original ACMG Summary
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant.
Gene: POLG (HGNC:9179)
Evidence Code: BP4 — Supporting
Agree to utilize REVEL, with thresholds of >0.75 and <0.15 for PP3 and BP4, respectively. Will also utilize POLG pathogenicity prediction server if/when live again (PMID: 28480171); both tools (REVEL and server) will have to be in agreement to score
Gene: POLG (HGNC:9179)
Evidence Code: BP5 — Original ACMG Summary
Variant found in a case with an alternate molecular basis for disease.
Gene: POLG (HGNC:9179)
Evidence Code: BP5 — Supporting
Variant found in a case with an alternate molecular basis for disease
Gene: POLG (HGNC:9179)
Evidence Code: BP6 — Original ACMG Summary
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: POLG (HGNC:9179)
Evidence Code: BP7 — Original ACMG Summary
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
Gene: POLG (HGNC:9179)
Evidence Code: BP7 — Supporting
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Gene: ETHE1 (HGNC:23287)
Evidence Code: PVS1 — Original ACMG Summary
Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
Caveats:
 • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7).
 • Use caution interpreting LOF variants at the extreme 3’ end of a gene.
 • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact.
 • Use caution in the presence of multiple transcripts.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PVS1 — Very Strong
Applied per PVS1 flowsheet of Abou Toyoun et al.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS1 — Original ACMG Summary
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Example: Val->Leu caused by either G>C or G>T in the same codon.
Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS1 — Strong
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS2 — Original ACMG Summary
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS2 — Strong
De novo in a patient with the disease and no family history
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS3 — Supporting
Reduced ETHE1 persulfide dioxygenase
Gene: ETHE1 (HGNC:23287)
Evidence Code: PS4 — Original ACMG Summary
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.
Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance.
Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM1 — Original ACMG Summary
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM2 — Original ACMG Summary
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Caveat: Population data for indels may be poorly called by next generation sequencing.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM2 — Moderate
<0.00002 (<0.0020%)
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM3 — Original ACMG Summary
For recessive disorders, detected in trans with a pathogenic variant
Note: This requires testing of parents (or offspring) to determine phase.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM3 — Moderate
Use per SVI guidance
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM4 — Original ACMG Summary
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM4 — Moderate
Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM5 — Original ACMG Summary
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Example: Arg156His is pathogenic; now you observe Arg156Cys.
Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM5 — Moderate
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM6 — Strong
De novo in a patient with the disease and no family history
Gene: ETHE1 (HGNC:23287)
Evidence Code: PM6 — Moderate
Assumed de novo, but without confirmation of paternity and maternity
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP1 — Original ACMG Summary
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
Note: May be used as stronger evidence with increasing segregation data.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP1 — Supporting
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP2 — Original ACMG Summary
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP3 — Original ACMG Summary
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP3 — Supporting
No gene-specific predictors; agree to utilize REVEL, with thresholds of >0.75 and <0.15 f or PP3 and BP4, respectively
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP4 — Moderate
Individual has abnormally high urinary ethylmalonic acid AND one of the following: 
(1) All of the following symptoms present: -Acrocyanosis -Petechiae -Chronic diarrhea -Developmental delay 
(2) ≥3 or more of the following biochemical studies: -Abnormally high blood C4-Acylcarnitine esters -Abnormally high blood C5-acylcarnitine -Abnormally high plasma thiosulphate -Abnormally low cytochrome oxidase activity in skeletal muscle (without evidence of other complexes decreased)
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP4 — Supporting
Individual has abnoramlly high urinary ethylmalonic acid AND one of the following: 
(1) 3 of the following features present: -Acrocyanosis -Petechiae -Chronic diarrhea -Developmental delay 
(2) abnormal laboratory studies in 2 of the following biochemical studies: -Abnormally high blood C4-Acylcarnitine esters -Abnormally high blood C5-acylcarnitine -Abnormally high plasma thiosulphate -Abnormally low cytochrome oxidase activity in skeletal muscle, without evidence of other complexes decreased
Gene: ETHE1 (HGNC:23287)
Evidence Code: PP5 — Original ACMG Summary
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BA1 — Stand Alone
0.001 (>0.1%)
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS1 — Strong
0.0002 (>0.020%)
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS2 — Original ACMG Summary
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS2 — Strong
Observed in a healthy adult individual in the homozygous state
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS2 — Supporting
Normal laboratory values (specific labs outlined in PP4)
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS4 — Original ACMG Summary
Lack of segregation in affected members of a family.
Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BS4 — Strong
Lack of segregation in affected and/or treated members of a family.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP1 — Original ACMG Summary
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP2 — Original ACMG Summary
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP2 — Supporting
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP3 — Original ACMG Summary
In frame-deletions/insertions in a repetitive region without a known function.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP3 — Supporting
In-frame deletions/insertions in a repetitive region without a known function
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP4 — Original ACMG Summary
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP4 — Supporting
No gene-specific predictors; agree to utilize REVEL, with thresholds of >0.75 and <0.15 f or PP3 and BP4, respectively
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP5 — Original ACMG Summary
Variant found in a case with an alternate molecular basis for disease.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP5 — Supporting
Variant found in a case with an alternate molecular basis for disease
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP6 — Original ACMG Summary
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP7 — Original ACMG Summary
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
Gene: ETHE1 (HGNC:23287)
Evidence Code: BP7 — Supporting
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved