owencqueen/cgbench_data huggingface dataset:
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PS1 — Strong
Modification Type: No change
No cardiomyopathy specifications. Apply as outlined by Richards 
et al
. 2015
1
.


Example of when rule should NOT be applied. NM_000256.3(
MYBPC3
): c.2308G>A (p.Asp770Asn) has an established impact on splicing leading to nonsense mediated decay (NMD) and should not be used to provide evidence for other variants observed to result in the same amino acid change.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PS2 — Strong
Modification Type: Disease-specific
Refer to SVI guidance on number/combination of cases required based on phenotype specificity
2
.


For most cardiomyopathies, it is recommended to default to 
Phenotype consistency: “Phenotype consistent with gene but not highly specific”
. Clinical judgment is required for shifting to a higher or lower category. 


For use as a STRONG or VERY STRONG criterion, ideally parents have been thoroughly clinically evaluated without evidence of cardiomyopathy (ideally using a combination of ECG and echocardiogram or cardiac MRI for maximum sensitivity).


A family history consistent with 
de novo
 inheritance should not have any clinical signs or symptoms suggestive of cardiomyopathy in a 1
st
 or 2
nd
 degree relative, for example: 




Sudden death under 60 years of age


Heart transplant


Implantable cardiac defibrillator (ICD) under 60 years of age


Features of cardiomyopathy (e.g., systolic dysfunction, hypertrophy, left ventricular enlargement in an individual without risk factors).


Other related/overlapping cardiomyopathies




Examples of non-suspicious family history may include non-specific clinical features (e.g., palpitations, syncope, borderline/inconclusive echocardiogram findings, heart attack if age appropriate and suspected to result from coronary artery disease), but every attempt should be made to clarify features. 


Generally, this criterion is only applicable in the ABSENCE of any other possible disease-causing variants.  If other pathogenic or likely pathogenic variants are present, consider decreasing points assigned or overall weight.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PS3 — Strong
Modification Type: Disease-specific
In vitro splicing assays (e.g., RNA studies)


In vitro
 splicing assays may be considered as 
STRONG
 evidence, providing the following criteria are met.




Prior knowledge of predominant transcripts in cardiac tissue




Analysis undertaken using RNA extracted from cardiac tissue from the individual with the variant


Analysis undertaken using RNA extracted from whole blood providing the relevant transcripts (isoforms) are expressed in blood and are at sufficient levels to assess splice disruption.


Assay shows a clear, reproducible and convincing effect on splicing (i.e. a distinct splice product, present at a level comparable to the splice product from the wild-type allele), which is not observed in controls




Confirmation of abnormal splice product by Sanger sequencing




NOTE:
 Mini-gene assay in non-patient derived cell lines are NOT considered to provide STRONG evidence.


NOTE:
  Whether to activate this rule needs to be reconciled with the variant spectrum and disease mechanism for the gene at hand (i.e., consider whether the effect is likely to lead to LOF or an in-frame alteration and whether this type of effect is expected to be disease causing) (Abou Tayoun 
et al.
 2018
3
).
Gene: TPM1 (HGNC:12010)
Evidence Code: PS3 — Moderate
Modification Type: Disease-specific
In vivo models (e.g., variant knock-in animal models)


Mammalian variant-specific knock-in animal models that produce a phenotype consistent with the clinical phenotype in humans (e.g., structural and/or functional cardiac abnormalities, premature death, arrhythmia) may be considered as 
MODERATE
 evidence


NOTE:
 The following assays/models do NOT meet criteria




Assays that are known to be associated with non-specific cardiac phenotypes (e.g., morpholino-induced pericardial edema in zebrafish)


In vivo evidence that is not variant specific, such as whole gene alterations (i.e., cDNA or whole gene transgenic mice and whole or partial gene knock-out mice)
Gene: TPM1 (HGNC:12010)
Evidence Code: PS3 — Supporting
Modification Type: Disease-specific
In vitro
 
assays (e.g., biochemical assays of myofilament function, motility assays, human iPSC-CM)


While some 
in vitro
 assays may provide evidence that a variant in a cardiomyopathy gene has an effect on protein and/or myofilament function, at present, there are no validated “gold-standard” assays that are considered to reliably predict the clinical phenotype.


As such, in the cardiomyopathy genes listed in these guidelines, data from individual 
in vitro
 studies are unlikely to meet the criteria required to assign this rule at more than SUPPORTING level.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PM2 — Supporting
Modification Type: Disease-specific
The values used to calculate the PM2 thresholds were derived from studies in Northern European populations that have been relatively well-characterized with regards to disease prevalence and variant spectrum. These thresholds can be applied to any population where disease prevalence is considered comparable (1/500 or lower), where the most frequent pathogenic variant accounts for no more than 2% of cases (e.g., has an allele frequency of ≤0.02 in cases based on the upper bound of 95% CI), and where the penetrance of a pathogenic variant is expected to be at least 50% (Kelly 
et al.
 2018
10
).


A threshold of 
≤0.00004
 in the subpopulation with the highest frequency when using the upper bound of the 95% CI activates this rule.




Alternatively, this is equivalent to the variant NOT being observed more than once (≤1 allele) in gnomAD v.2.1.1 in one of the non-founder populations (e.g., absence required from the Other and Ashkenazi Jewish subpopulations).


Applying a threshold of ≤0.00004 (upper bound of 95% CI of the allele frequency in gnomAD) is equivalent to the variant being seen in a single subpopulation and that subpopulation meets any of the following:


Allele Count (AC) in Allele Number (AN)


≤1 in ≥120,000


≤2 in ≥160,000


≤3 in ≥195,000


≤4 in ≥230,000








gnomAD is the preferred database for this calculation, but currently only displays the filtering allele frequency (FAF), which is equivalent to a lower bound estimate of the 95% CI, when the upper bound is what is needed.




Confidence interval tools, such as 
Confit-de-MAF
, can be used to determine the upper bound of the 95% CI of the observed allele frequency.




Due to current technical limitations of next generation sequencing technologies, minor allele frequencies for complex variants (e.g., large indels) may not be accurately represented in population databases.


Caution should be used when a variant is only identified, or over-represented, in one of the smaller gnomAD populations, as the gnomAD allele frequencies may not accurately represent the true population frequency.


Population databases may contain affected or pre-symptomatic individuals for diseases with reduced penetrance/variable onset.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PM4 — Moderate
Modification Type: General recommendation
Strength of rule should be carefully considered and may require downgrading to SUPPORTING based on the predicted impact of the variant, including the size of the deletion/insertion, its location, and conservation of the region. 


For genes where PVS1 is not applicable (i.e., where there is no evidence that pLOF variants cause disease), consider using this rule at MODERATE or SUPPORTING strength for truncating variants that do NOT undergo nonsense mediated decay (NMD).
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PM5 — Moderate
Modification Type: General recommendation
This criterion can be used at MODERATE if a different missense variant at the same codon has been classified as 
pathogenic
 using these modified guidelines without application of PM5.


The impact of the amino acid change being evaluated needs to be compared to the impact of the amino acid change that is established as pathogenic (e.g., a change of Ala to His is less severe than Ala to Cys change). Consider reducing the strength of this rule to SUPPORTING if the predicted impact is not expected to be equivalent or more severe.


PM5 should not be combined with PM1.  If both are applicable at MODERATE weight, use of PM5 is most appropriate since it is variant specific.
Gene: TPM1 (HGNC:12010)
Evidence Code: PM5 — Supporting
Modification Type: General recommendation
This criterion can be considered at SUPPORTING if a different missense variant at the same codon has been classified as 
likely pathogenic
 using these modified guidelines without application of PM5.


The impact of the amino acid change being evaluated needs to be compared to the impact of the amino acid change that is established as likely pathogenic (e.g., a change of Ala to His is less severe than Ala to Cys change). Consider reducing the strength of this rule to NOT APPLICABLE if the predicted impact is not expected to be equivalent or more severe.


PM5 should not be combined with PM1.  The one with the higher strength should be applied, but if both are applicable at SUPPORTING weight, use of PM5 is most appropriate since it is variant specific.
Gene: TPM1 (HGNC:12010)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: TPM1 (HGNC:12010)
Evidence Code: PM6 — Moderate
Modification Type: Disease-specific
Refer to SVI guidance on number/combination of cases required based on phenotype specificity
2
.


For most cardiomyopathies, it is recommended to default to “phenotype consistent with gene but not highly specific”. Clinical judgment is required for shifting to a higher or lower phenotypic consistency. 


See PS2 for additional considerations.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PP1 — Strong
Modification Type: Disease-specific
Due to the genotypic and phenotypic heterogeneity of inherited cardiomyopathies, segregation thresholds have been conservatively set at 
≥7
 
segregations
 (LOD score of 2.1) for 
STRONG
.


Although rare for inherited cardiomyopathies, when the phenotype/presentation of a variant within and across families is highly specific (e.g., early-onset severe RCM in all affected individuals), the following thresholds as proposed by Jarvik and Browning (2016)
11
 can be considered: 




STRONG evidence requires ≥5 segregations (LOD score of 1.5)




Only genotype positive/phenotype positive individuals are counted as segregations, which can include affected obligate carriers. Genotype positive/phenotype negative individuals are generally less informative for cardiomyopathy genes due to variable age at onset and reduced penetrance.


Phenotypes should be clinically confirmed, whenever possible, and should not include individuals with a suspected diagnosis.  


Important considerations include:




Segregation of a variant within a single family or haplotype has the potential to represent linkage disequilibrium with another undetected variant.  If linkage disequilibrium is a concern, consider downgrading strength of segregation. 


Use of segregation criteria should be carefully evaluated if variant frequency meets criteria for BS1.


Caution is needed when counting segregations in presence of other possible disease-causing variants, as both variants may be contributing to the phenotype. 


Caution is needed when distantly related (≥3
rd
 degree) affected individuals are connected by unknown or unaffected relatives (raises possibility of multiple causes of disease).
Gene: TPM1 (HGNC:12010)
Evidence Code: PP1 — Moderate
Modification Type: Disease-specific
Due to the genotypic and phenotypic heterogeneity of inherited cardiomyopathies, segregation thresholds have been conservatively set at 
≥5
 
segregations
 (LOD score of 1.5) for 
MODERATE
.


Although rare for inherited cardiomyopathies, when the phenotype/presentation of a variant within and across families is highly specific (e.g., early-onset severe RCM in all affected individuals), the following thresholds as proposed by Jarvik and Browning (2016)
11
 can be considered: 




MODERATE evidence requires ≥4 segregations (LOD score of 1.2)




Only genotype positive/phenotype positive individuals are counted as segregations, which can include affected obligate carriers. Genotype positive/phenotype negative individuals are generally less informative for cardiomyopathy genes due to variable age at onset and reduced penetrance.


Phenotypes should be clinically confirmed, whenever possible, and should not include individuals with a suspected diagnosis.  


Important considerations include:




Segregation of a variant within a single family or haplotype has the potential to represent linkage disequilibrium with another undetected variant.  If linkage disequilibrium is a concern, consider downgrading strength of segregation. 


Use of segregation criteria should be carefully evaluated if variant frequency meets criteria for BS1 (see below).


Caution is needed when counting segregations in presence of other possible disease-causing variants, as both variants may be contributing to the phenotype. 


Caution is needed when distantly related (≥3
rd
 degree) affected individuals are connected by unknown or unaffected relatives (raises possibility of multiple causes of disease).
Gene: TPM1 (HGNC:12010)
Evidence Code: PP1 — Supporting
Modification Type: Disease-specific
Due to the genotypic and phenotypic heterogeneity of inherited cardiomyopathies, segregation thresholds have been conservatively set at 
≥3
 
segregations
 (LOD score of 0.9) for 
SUPPORTING
. The thresholds as proposed by Jarvik and Browning (2016)
11
 are the same at ≥3 segregations (LOD score of 0.9) for supporting.


Only genotype positive/phenotype positive individuals are counted as segregations, which can include affected obligate carriers. Genotype positive/phenotype negative individuals are generally less informative for cardiomyopathy genes due to variable age at onset and reduced penetrance.


Phenotypes should be clinically confirmed, whenever possible, and should not include individuals with a suspected diagnosis.  


Important considerations include:




Segregation of a variant within a single family or haplotype has the potential to represent linkage disequilibrium with another undetected variant.  If linkage disequilibrium is a concern, consider downgrading strength of segregation. 


Use of segregation criteria should be carefully evaluated if variant frequency meets criteria for BS1 (see below).


Caution is needed when counting segregations in presence of other possible disease-causing variants, as both variants may be contributing to the phenotype. 


Caution is needed when distantly related (≥3
rd
 degree) affected individuals are connected by unknown or unaffected relatives (raises possibility of multiple causes of disease).
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PP2 — Supporting
Modification Type: Disease-specific,Gene-specific
Application of this rule takes into consideration empirical data quantifying levels of rare missense variant enrichment in HCM referral cohorts compared to population-based cohorts (Walsh 
et al.
 2019
12
) rather than the missense constraint score in gnomAD. 


On the basis of data from Walsh 
et al.
 2019
12
, 
PP2 is currently
 
only applicable to
 
TPM1
 
for HCM
 (transcripts ENST00000403994 and NM_001018005.2)
.


Data from HCM case cohorts was used to derive these cluster regions. Therefore, this rule should NOT be applied when additional evidence for the variant supports that the variant causes a phenotype other than HCM (e.g., variant seen in multiple DCM cases).


Enrichment was not observed for DCM in any genes.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: PP3 — Supporting
Modification Type: Disease-specific
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. Meta-predictors, such as REVEL, are preferred over multiple individual predictors.


Use of REVEL (Ioannidis 
et al.
 2016
13
) is recommended at thresholds of 
≥0.70 for PP3
.


Clinical judgment is needed if any individual algorithms or conservation data are contradictory to REVEL data.


Positive predictive value for benign/no impact predictions is generally higher than for pathogenic/impact predictions.


SpliceAI
14
 is recommended for evaluation of predicted splice impacts.
Gene: TPM1 (HGNC:12010)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: TPM1 (HGNC:12010)
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: TPM1 (HGNC:12010)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Gene: TPM1 (HGNC:12010)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
Allele frequency is 
≥0.001
 based on the 
filtering allele frequency (FAF)
 in 
gnomAD
 in the subpopulation with the highest frequency (popmax).


The values used to calculate the BA1 threshold were derived from studies in Northern European populations that have been relatively well-characterized with regards to disease prevalence and variant spectrum. These thresholds can be applied to any population where disease prevalence is considered comparable (1/300 or lower).


The threshold is applicable when assessing variants in the context of autosomal dominant cardiomyopathy. 


gnomAD is the preferred database for this calculation. If a subpopulation specific FAF other than the popmax is needed, this value can be calculated using the AlleleFrequencyApp on the 
CardioDB website
.




Using the Inverse AF tab, enter in the population size and the number of alleles identified and it will calculate the FAF.  


Set confidence to 0.95 (95%).


If the FAF is ≥0.001, this rule can be applied.




The FAF by platform (e.g., exome vs. genome; v.2.1.1 vs. v.3.1.1) should be considered, the larger population is most likely to have the most accurate representation of “true” population allele frequency.


Caution is needed when considering any population cohorts that are smaller than the smallest subpopulations within gnomAD v.2.1.1 (e.g., ~5000 individuals or ~10,000 alleles). Despite this conservative nature of this threshold and approach, in smaller cohorts, the observed allele frequency may less accurately reflect the true allele frequency. Traditionally, once a variant is classified as Benign, it is rarely re-evaluated and so the highest confidence is needed to establish that classification on an allele frequency alone.
Gene: TPM1 (HGNC:12010)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: TPM1 (HGNC:12010)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific,Gene-specific
Allele frequency is 
≥0.0001 for
 
TPM1
 based on the 
filtering allele frequency (FAF)
 in 
gnomAD
 in the subpopulation with the highest frequency (popmax).


Criterion BS1 may only be used as standalone evidence to classify a variant as Likely Benign in the absence of conflicting data. See SVI guidance (Tavtigian 
et al.
 2018
15
; Tavtigian 
et al.
 2020
16
). 


See BA1 for additional specifications that also apply to BS1.
Gene: TPM1 (HGNC:12010)
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.