owencqueen/cgbench_data huggingface dataset:
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PVS1 — Very Strong
Null variant in a gene where LOF is a known mechanism of disease.


Per modified RUNX1 PVS1 decision tree for SNVs and CNVs and table of splicing effects.


Comments:


RUNX1 LOF variants are a common mechanism of disease in FPD/AML. Three major isoforms (A, B, C) are expressed by use of two promotors and alternative splicing. C-terminal variants not predicted to undergo NMD are classified as PVS1_strong, deletions of exons 2 and 3, presumably only affecting RUNX1 isoform 1C,  meet PVS1_moderate.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PVS1 — Strong
Null variant in a gene where LOF is a known mechanism of disease.


Per modified RUNX1 PVS1 decision tree for SNVs and CNVs and table of splicing effects.


Comments:


RUNX1 LOF variants are a common mechanism of disease in FPD/AML. Three major isoforms (A, B, C) are expressed by use of two promotors and alternative splicing. C-terminal variants not predicted to undergo NMD are classified as PVS1_strong, deletions of exons 2 and 3, presumably only affecting RUNX1 isoform 1C,  meet PVS1_moderate.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PVS1 — Moderate
Null variant in a gene where LOF is a known mechanism of disease.


Per modified RUNX1 PVS1 decision tree for SNVs and CNVs and table of splicing effects.


Comments:


RUNX1 LOF variants are a common mechanism of disease in FPD/AML. Three major isoforms (A, B, C) are expressed by use of two promotors and alternative splicing. C-terminal variants not predicted to undergo NMD are classified as PVS1_strong, deletions of exons 2 and 3, presumably only affecting RUNX1 isoform 1C,  meet PVS1_moderate.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PS1 — Strong
Same AA change as a previously established pathogenic variant regardless of nucleotide change.


Comments:


RNA data or agreement in splicing predictors show no splicing effects (SSF and MES predict either increase in canonical splice site score or decrease of  canonical splice score by no more than 10% and no putative splice site are created).


The previously established PATH/LPATH variant must be asserted pathogenic/likely pathogenic based on MM-VCEP rules for RUNX1 before this rule can be applied
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS1 — Moderate
Same AA change as a previously established likely pathogenic variant regardless of nucleotide change.


Comments:


RNA data or agreement in splicing predictors show no splicing effects (SSF and MES predict either increase in canonical splice site score or decrease of  canonical splice score by no more than 10% and no putative splice site are created).


The previously established PATH/LPATH variant must be asserted pathogenic/likely pathogenic based on MM-VCEP rules for RUNX1 before this rule can be applied
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PS2 — Moderate
≥ 2 proven de novo occurrences (maternity and paternity confirmed) in patients with the RUNX1-phenotype.


Comments:


No family history is defined as: absence of the variant and any of the RUNX1-phenotypic criteria in first- or second degree relatives.


The proband must exhibit at least one phenotypic FPD/AML criterion. (3) The maximum allowable strength by combining PS2 and PM6 criteria is to apply one moderate or two supporting rules.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS2 — Supporting
1 proven de novo occurrence (maternity and paternity confirmed) in a patient with the RUNX1-phenotype.


Comments:


No family history is defined as: absence of the variant and any of the RUNX1-phenotypic criteria in first- or second degree relatives.


The proband must exhibit at least one phenotypic FPD/AML criterion. (3) The maximum allowable strength by combining PS2 and PM6 criteria is to apply one moderate or two supporting rules.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PS3 — Strong
Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) AND data from a secondary assay demonstrating altered function.


PS3 cannot be applied if the variant meets PVS1. If the variant meets criteria for PVS1_strong and PS3, we recommend applying either PS3_moderate or upgrading PVS1_strong to PVS1 without applying PS3 .
 Comments:


Transactivation assays should include wt and known pathogenic controls, as well as co-expression with CBFβ. Promoter sequences of CSF1R (M-CSF-R), PF4, C-FMS and GZMB, containing consensus RUNX1 binding sites have been used for transactivation assays.


The following secondary assays have been performed: EMSA and yeast hybrid assays (decreased DNA-binding affinity), co-IP, FRET and affinity assays (diminished heterodimerization ability with CBFβ), IF and WB with cell fractionation (abnormal cellular localization), colony forming assays (reduced colony-forming potential), xenotransplantation experiments (abnormal function of mutant RUNX1 in vivo).


PS3 can also be applied for evidence of very low or abnormal mRNA/protein expression of the variant allele as a functional consequence of a null variant or incorrect mRNA/protein products
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS3 — Moderate
Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) OR ≥ 2 secondary assays demonstrating altered function.


Comments:


Transactivation assays should include wt and known pathogenic controls, as well as co-expression with CBFβ. Promoter sequences of CSF1R (M-CSF-R), PF4, C-FMS and GZMB, containing consensus RUNX1 binding sites have been used for transactivation assays.


The following secondary assays have been performed: EMSA and yeast hybrid assays (decreased DNA-binding affinity), co-IP, FRET and affinity assays (diminished heterodimerization ability with CBFβ), IF and WB with cell fractionation (abnormal cellular localization), colony forming assays (reduced colony-forming potential), xenotransplantation experiments (abnormal function of mutant RUNX1 in vivo).


PS3 can also be applied for evidence of very low or abnormal mRNA/protein expression of the variant allele as a functional consequence of a null variant or incorrect mRNA/protein products
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS3 — Supporting
Transactivation assays demonstrating enhanced transactivation (>115% of wt).


Comments:


Transactivation assays should include wt and known pathogenic controls, as well as co-expression with CBFβ. Promoter sequences of CSF1R (M-CSF-R), PF4, C-FMS and GZMB, containing consensus RUNX1 binding sites have been used for transactivation assays.


The following secondary assays have been performed: EMSA and yeast hybrid assays (decreased DNA-binding affinity), co-IP, FRET and affinity assays (diminished heterodimerization ability with CBFβ), IF and WB with cell fractionation (abnormal cellular localization), colony forming assays (reduced colony-forming potential), xenotransplantation experiments (abnormal function of mutant RUNX1 in vivo).


PS3 can also be applied for evidence of very low or abnormal mRNA/protein expression of the variant allele as a functional consequence of a null variant or incorrect mRNA/protein products
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PS4 — Strong
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.


≥ 4 probands meeting RUNX1-phenotypic criteria.


Comments:


The affected individual has to fit at least one of the RUNX1-phenotypic criteria AND variant has to be either absent from gnomAD (overall population) or only present once.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS4 — Moderate
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.


2-3 probands meeting RUNX1-phenotypic criteria.


Comments:


The affected individual has to fit at least one of the RUNX1-phenotypic criteria AND variant has to be either absent from gnomAD (overall population) or only present once.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PS4 — Supporting
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.


1 proband meeting RUNX1-phenotypic criteria.


Comments:


The affected individual has to fit at least one of the RUNX1-phenotypic criteria AND variant has to be either absent from gnomAD (overall population) or only present once.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PM1 — Moderate
Located in a mutational hot spot and/or critical and well-established functional domain without benign variation.


Variant affecting one of the following 13 hotspot residues: R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204.


Comments:


The RHD (AA 77-204) has been established as highly conserved DNA-binding domain without any benign variation in ClinVar. Residues in the region (AA 77-104) are also in the RHD, but no germline variants have been reported to date. The AA range under PM1_supporting may be expanded in the future to other parts of the protein if more evidence emerges.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM1 — Supporting
Located in a mutational hot spot and/or critical and well-established functional domain without benign variation.


Variant affecting one of the other AA residues 105-204 within the RHD.


Comments:


The RHD (AA 77-204) has been established as highly conserved DNA-binding domain without any benign variation in ClinVar. Residues in the region (AA 77-104) are also in the RHD, but no germline variants have been reported to date. The AA range under PM1_supporting may be expanded in the future to other parts of the protein if more evidence emerges.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PM2 — Moderate
Absent from controls.


Per original ACMG/AMP guidelines.


Comments:


Variant must be completely absent from all population databases.  The mean coverage of RUNX1 in the population database used should be at least 20x.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PM4 — Moderate
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.


In-frame deletion/insertion impacting at least one of the 13 hotspot residues R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201


Comments:


See PM1
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM4 — Supporting
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.


Other in-frame deletion/insertion impacting residues 105-204 within the RHD.


Comments:


See PM1
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PM5 — Strong
Missense change at the same residue where ≥ 2  different missense changes have previoulsy been determined to be pathogenic. PM5_strong cannot be applied together with PM1.


Comments:


see PS1
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM5 — Moderate
Missense change at the same residue where a different missense change has previously been determined to be pathogenic.


Comments:


see PS1
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM5 — Supporting
Missense change at the same residue where a different missense change has previously been determined to be likely pathogenic.


Comments:


see PS1
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM6 — Moderate
Assumed de novo (but without confirmation of maternity and paternity) in a patient with the disease and no family history.


≥ 4 assumed de novo occurrences (without confirmation of maternity and paternity) in patients with the RUNX1-phenotype.


Comments:


see PS2
Gene: RUNX1 (HGNC:10471)
Evidence Code: PM6 — Supporting
Assumed de novo (but without confirmation of maternity and paternity) in a patient with the disease and no family history.


2 or 3 assumed de novo occurrences (without confirmation of maternity and paternity) in patients with the RUNX1-phenotype.


Comments:


see PS2
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PP1 — Strong
Co-segregation with disease in multiple affected family members.


≥ 7 meioses observed within one or across multiple families.


Comments:


Affected individuals show at least one of the RUNX1-specific phenotypic criteria.


Only genotype and phenotype positive individuals and obligate carriers are counted.


Demonstration of co-segregation in multiple families is not required since many RUNX1 variants are unique and only occur in one family.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PP1 — Moderate
Co-segregation with disease in multiple affected family members.


5 or 6 meioses observed within one or across multiple families.


Comments:


Affected individuals show at least one of the RUNX1-specific phenotypic criteria.


Only genotype and phenotype positive individuals and obligate carriers are counted.


Demonstration of co-segregation in multiple families is not required since many RUNX1 variants are unique and only occur in one family.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PP1 — Supporting
Co-segregation with disease in multiple affected family members.


3 or 4 meioses observed within one or across multiple families.


Comments:


Affected individuals show at least one of the RUNX1-specific phenotypic criteria.


Only genotype and phenotype positive individuals and obligate carriers are counted.


Demonstration of co-segregation in multiple families is not required since many RUNX1 variants are unique and only occur in one family.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: PP3 — Supporting
Multiple lines of computational evidence support a deleterious effect on the gene or gene product.


Comments:


PP3 should be applied for missense variants with a REVEL score of >0.75.


PP3 should also be applied for missense or synonymous variants if the variant alters the last three bases of an exon preceding a splice donor site or the first three bases of an exon following an acceptor splice site and the predicted decrease in the score of the canonical splice site (measured by both MES and SSF) is at least 75% regardless of the predicted creation/presence of a putative cryptic splice site.


PP3 should also be applied for intronic variants (in introns 4-8) located in reference to exons at positions +3 to +5 for donor splice sites or -3 to -5 for acceptor splice sites and the predicted decrease in the score of the canonical splice site is at least 75% (measured by both MES and SSF) regardless of the predicted creation/presence of a putative cryptic splice site.


PP3 cannot be applied for canonical splice site variants.
Gene: RUNX1 (HGNC:10471)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium
Gene: RUNX1 (HGNC:10471)
Evidence Code: BA1 — Stand Alone
Allele frequency is >5% in ESP, 1000G, or ExAC.


Comments:


The variant is present in in any general continental population dataset with a minimum number of 2,000 alleles and variant present in ≥ 5 alleles.
Gene: RUNX1 (HGNC:10471)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: RUNX1 (HGNC:10471)
Evidence Code: BS1 — Strong
Allele frequency is greater than expected for disorder.


MAF between 0.00015 (0.015%) and 0.0015 (0.15%)


Comments:


The variant is present in any general continental population dataset with a minimum number of 2,000 alleles and variant present in ≥ 5 alleles.


Variant can be classified as likely benign based on BS1 alone if there is no contradictory evidence supporting pathogenicity.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: BS3 — Strong
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.


Transactivation assays demonstrating normal transactivation (80-115% of wt) AND


data from a secondary assay demonstrating normal function.


Comments:


see PS3 (1) and (2)
Gene: RUNX1 (HGNC:10471)
Evidence Code: BS3 — Supporting
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.


Transactivation assays demonstrating normal transactivation (80-115% of wt).


Comments:


see PS3 (1) and (2)
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: BS4 — Strong
Lack of segregation in affected members of a family.


Applied when seen in ≥ 2 informative meioses.


Comments:


This code should only be applied for genotype-positive, phenotype-negative (with sufficient laboratory evidence) family members.
Gene: RUNX1 (HGNC:10471)
Evidence Code: BP1 — Original ACMG Summary
Missense variant in a gene for which primarily truncating variants are known to cause disease
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
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.


Per original ACMG/AMP guidelines.


Comments:


BP2 can also be applied if the variant is detected in a homozygous state.
Gene: RUNX1 (HGNC:10471)
Evidence Code: BP3 — Original ACMG Summary
In frame-deletions/insertions in a repetitive region without a known function.
Gene: RUNX1 (HGNC:10471)
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: RUNX1 (HGNC:10471)
Evidence Code: BP4 — Supporting
Multiple lines of computational evidence suggest no impact on gene or gene product.


Comments:


BP4 should be applied for missense variants with a REVEL score < 0.15 as well as synonymous, intronic and non-coding variants for which SSF and MES predict either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created.
Gene: RUNX1 (HGNC:10471)
Evidence Code: BP5 — Original ACMG Summary
Variant found in a case with an alternate molecular basis for disease.
Gene: RUNX1 (HGNC:10471)
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.