NF1 c.7584A>G, p.(Gln2528=)

Reasoning

The NF1 framework identifies autosomal-dominant NF1, and gnomAD v4.1 reports six homozygotes for this allele (overall AF 0.000977675; 1578/1614034 alleles; 5 exome homozygotes and 1 genome homozygote). Homozygous occurrence in a large population dataset is strongly inconsistent with a highly penetrant autosomal-dominant NF1 disease allele and supports BS2 at strong strength. This is subject to human review because gnomAD does not provide individual-level NF1 phenotype, age, or ascertainment data needed to confirm that every homozygote is an unaffected healthy adult. The gnomAD v2.1 all-comers and non-cancer exome subsets each report zero homozygotes, while gnomAD v3.1 non-cancer reports one genome homozygote.

Rule

{'source': 'generic_acmg_amp', 'publication': 'PMID:25741868', 'criterion': 'BS2', 'population_source': 'all-comers gnomAD default because no applicable VCEP subset rule was supplied'}

Evidence considered

• The governing NF1 framework identifies autosomal-dominant inheritance for neurofibromatosis type 1.
• gnomAD v4.1 reports total_hom 6, comprising 5 exome homozygotes and 1 genome homozygote, among 1578/1614034 observed alleles.
• The absence of individual-level phenotype and age data prevents direct confirmation of the ACMG/AMP healthy-adult wording and is the reason for human review.
• gnomAD v2.1 all-comers and non-cancer exomes report zero homozygotes; gnomAD v3.1 non-cancer genomes report one homozygote.

Still missing

• Individual-level phenotype and age information for the six gnomAD v4.1 homozygotes is unavailable.

Sources

Reasoning

The variant is synonymous (NM_001042492.2:c.7584A>G; p.(Gln2528=)), so BP4 is evaluated through SpliceAI only. The governing NF1 framework was reviewed but contains no criterion-specific BP4 assignment. SpliceAI reports a maximum delta score of 0.001, which is at or below the supplied BP4 supporting threshold of 0.1, supporting no predicted splice impact. REVEL is absent but is not applicable to this non-missense variant, and the same SpliceAI result is not double-counted as PP3.

Rule

Synonymous variant: evaluate BP4 with SpliceAI only; BP4 supporting requires max delta <=0.1.

Evidence considered

• The case variant is NM_001042492.2:c.7584A>G, annotated as synonymous, NP_001035957.1:p.(Gln2528=).
• SpliceAI is available and reports maximum delta 0.001.
• The supplied Jaganathan et al. 2019 calibration (PMID:30661751) defines BP4 supporting for SpliceAI max delta <=0.1.

Sources

Reasoning

BP7 applies because the variant is synonymous: NM_001042492.2:c.7584A>G produces NP_001035957.1:p.(Gln2528=). The variant is not in a canonical splice-consensus position, and SpliceAI predicts minimal splice impact with a maximum delta score of 0.001, supporting that the synonymous change is unlikely to affect splicing. This is evaluated independently from PP3/BP4 without adding another computational code.

Rule

BP7 supporting: synonymous variant with no expected effect on splicing and outside a well-established splice consensus sequence.

Evidence considered

• The variant is synonymous, NM_001042492.2:c.7584A>G, p.(Gln2528=).
• The case assessment identifies the variant as outside the canonical splice consensus, and SpliceAI reports maximum delta 0.001.
• The ACMG/AMP guideline basis for BP7 is Richards et al. 2015 (PMID:25741868): a synonymous variant may support benign evidence when it is not expected to affect splicing.

Sources

Reasoning

The NF1 VCEP framework is present but contains no usable criterion-specific PS4 rule payload, so generic ACMG/AMP PS4 was considered. The exact synonymous variant NM_001042492.3:c.7584A>G (p.Gln2528=) is not mentioned in the reviewed NF1 clinical or AML literature: PMID:10678181 describes Nf1-deficient mouse leukemogenesis without this variant, and PMID:23460398 reports other NF1 alterations in 20 AML patients without this variant. No case-control enrichment, affected-case series, or statistically significant phenotype association for this exact variant is provided. Therefore PS4 is not met.

Rule

Generic PS4: statistically significant enrichment of the exact variant in affected individuals compared with controls, or a sufficiently convincing affected-case series; no applicable NF1-specific rule was available.

Evidence considered

• The NF1 VCEP record is available, but its extracted criterion-specific rule payload is empty and incomplete, so no NF1-specific PS4 threshold or rule could be applied.
• PMID:10678181 reports Nf1-deficient mouse hematopoietic models and JMML-like disease, but the exact variant c.7584A>G / p.Gln2528= is not mentioned.
• PMID:23460398 reports six other NF1 alterations in 7 of 20 de novo AML patients, but the exact variant c.7584A>G / p.Gln2528= is not mentioned.
• ClinVar contains exact-variant submissions, but no expert-panel classification and no case-control enrichment analysis for this variant.

Sources

Reasoning

No NF1-specific PM2 rule is supplied by the governing ClinGen NF1 framework, so the supplied generic SVI PM2 supporting threshold of <=0.0001 applies (ClinGen SVI, PMID:25741868). The variant is substantially more frequent than this threshold in every relevant dataset: gnomAD v4.1 overall AF 0.000977675, gnomAD v2.1 overall AF 0.00109648, gnomAD v2.1 non-cancer exomes AF 0.00111065, and gnomAD v3.1 non-cancer genomes AF 0.0012574. Therefore PM2 is not met.

Rule

{'source': 'generic_svi_default', 'publication': 'PMID:25741868', 'threshold': '<=0.0001', 'strength': 'supporting', 'population_source': 'all-comers gnomAD default because no applicable VCEP subset rule was supplied'}

Evidence considered

• The NF1 framework contains no criterion-specific PM2 threshold, so the supplied generic SVI PM2 threshold of <=0.0001 was applied (ClinGen SVI, PMID:25741868).
• gnomAD v4.1 all-comers overall AF is 0.0009776745719111246 (1578/1614034 alleles).
• gnomAD v2.1 all-comers overall AF is 0.0010964757148314258; its non-cancer exome AF is 0.0011106512723925033 (263/236798 alleles).
• gnomAD v3.1 non-cancer genome AF is 0.0012574024499067088 (186/147924 alleles).

Sources

Reasoning

The variant is synonymous (NM_001042492.2:c.7584A>G; p.(Gln2528=)), so the applicable PP3/BP4 path is SpliceAI rather than REVEL. The governing NF1 framework was reviewed but contains no criterion-specific PP3 assignment. SpliceAI is available and its maximum delta score is 0.001, below the supplied PP3 supporting threshold of 0.2 and the moderate threshold of 0.5; therefore PP3 is not met. The absent REVEL score is not relevant because this is not a missense variant, and no other predictor is used for this criterion.

Rule

Synonymous variant: evaluate PP3 with SpliceAI only; PP3 supporting requires max delta >=0.2 and PP3 moderate requires >=0.5.

Evidence considered

• The case variant is NM_001042492.2:c.7584A>G, annotated as synonymous, NP_001035957.1:p.(Gln2528=).
• SpliceAI is available with DS_AG 0.000, DS_AL 0.000, DS_DG 0.001, DS_DL 0.001, and maximum delta 0.001.
• For synonymous variants, the applicable path is SpliceAI only; the supplied Jaganathan et al. 2019 calibration (PMID:30661751) defines PP3 supporting at max delta >=0.2 and PP3 moderate at >=0.5.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact variant is represented in ClinVar, but the submission audit reports zero expert-panel submissions; the available classifications are laboratory submissions, including Likely benign and Benign, and are explicitly non-qualifying for PP5. Therefore PP5 is not met.

Rule

PP5 applies only to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• The exact variant match is confirmed in ClinVar, but the submission audit reports expert_panel_submissions = 0.
• Available ClinVar assertions are ordinary laboratory submissions, predominantly Likely benign or Benign, rather than an expert-panel Pathogenic or Likely pathogenic classification.
• No expert-panel Pathogenic or Likely pathogenic classification was identified; aggregate labels and non-expert assertions are excluded by the criterion rule.

Sources

Reasoning

No NF1-specific population threshold is provided by the governing ClinGen NF1 framework; therefore the generic ACMG/AMP BA1 threshold of >=0.05 applies (PMID:25741868). The highest all-comers gnomAD v4.1 population AF is 0.00909091 in the Middle Eastern XY subgroup, with overall AF 0.000977675 and grpmax FAF 0.0061424. These values are below 0.05, so BA1 is not met. The gnomAD v3.1 non-cancer HGDP:MOZABITE AF of 0.0769231 is based on only 4/52 alleles and is a small-subpopulation sampling artifact; it is not used to override the default all-comers source in the absence of a VCEP instruction selecting that subset.

Rule

{'source': 'generic_acmg_amp', 'publication': 'PMID:25741868', 'threshold': '>=0.05', 'population_source': 'all-comers gnomAD default because no applicable VCEP subset rule was supplied'}

Evidence considered

• The NF1 ClinGen framework is present but supplies no criterion-specific population rule or alternative frequency source, so the generic BA1 threshold of >=0.05 from ACMG/AMP (PMID:25741868) was used.
• gnomAD v4.1 reports overall AF 0.000977675 and the highest named population AF 0.007926023778071334 in Middle Eastern individuals (48/6056 alleles); grpmax FAF is 0.006142400000000011.
• gnomAD v2.1 reports overall AF 0.0010964757148314258 and grpmax FAF 0.00159181, also below BA1.
• The gnomAD v3.1 non-cancer HGDP:MOZABITE value of 0.0769231 is based on 4/52 alleles and was treated as a low-denominator ancestry artifact rather than a representative default population frequency.

Sources

Reasoning

No NF1-specific BS1 threshold is provided by the governing ClinGen NF1 framework, so the supplied generic SVI BS1 threshold of >=0.01 applies (Whiffin et al., PMID:28518168). The highest all-comers gnomAD v4.1 population AF is 0.00909091 in the Middle Eastern XY subgroup; the broader grpmax FAF is 0.0061424 and the overall AF is 0.000977675. All are below 0.01. The gnomAD v3.1 non-cancer HGDP:MOZABITE AF of 0.0769231 reflects only 4/52 alleles and is not used as a reliable population-wide BS1 trigger without a governing specification selecting that subset.

Rule

{'source': 'generic_svi_default', 'publication': 'PMID:28518168', 'threshold': '>=0.01', 'population_source': 'all-comers gnomAD default because no applicable VCEP subset rule was supplied'}

Evidence considered

• The governing NF1 framework contains no BS1-specific frequency threshold, so the supplied generic SVI threshold of >=0.01 was applied (Whiffin et al., PMID:28518168).
• gnomAD v4.1 reports overall AF 0.000977675, maximum named population AF 0.007926023778071334, and grpmax FAF 0.006142400000000011; none reaches 0.01.
• The gnomAD v3.1 non-cancer HGDP:MOZABITE AF of 0.0769231 is based on 4/52 alleles and was considered a low-denominator ancestry artifact rather than a robust default frequency estimate.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact variant is represented in ClinVar, but the submission audit reports zero expert-panel submissions; the available Benign and Likely benign labels are from ordinary laboratory submissions and therefore cannot trigger BP6. Thus BP6 is not met.

Rule

BP6 applies only to an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• The exact variant match is confirmed in ClinVar, but the submission audit reports expert_panel_submissions = 0.
• ClinVar contains Benign and Likely benign ordinary laboratory submissions, including single-submitter records, but none is an expert-panel assertion.
• Aggregate ClinVar labels and non-expert laboratory assertions are excluded by the BP6 rule.

Sources

Reasoning

PS2 cannot be assessed because the available case evidence does not document a confirmed de novo occurrence in the proband, including validated parental genotypes and maternity/paternity confirmation. The variant is annotated as NM_001042492.2:c.7584A>G (p.Gln2528=), but variant identity alone does not establish de novo status. The NF1-specific CSPEC is present but contains no usable criterion-specific rule payload, so the generic ACMG/AMP framework is used; it requires direct de novo evidence that is absent here.

Evidence considered

• The case materials identify the variant as NM_001042492.2:c.7584A>G (NP_001035957.1:p.(Gln2528=)) but provide no proband-parent trio result or confirmed de novo observation.
• The NF1-specific CSPEC record is available, but its retrieved rule payload contains no criterion-specific PS2 instruction; generic ACMG/AMP guidance was therefore applied.
• No paper_extracts entry documents this exact variant in a de novo proband-parent study.

Still missing

• Proband genotype confirmation linked to the family study
• Both parental genotypes from validated testing
• Maternity and paternity confirmation
• Assessment for parental mosaicism where relevant

Sources

Reasoning

The NF1 ClinGen specification record is present but contains no PS3-specific rules. Generic ACMG/AMP guidance recognizes well-established functional assays, including mRNA studies, as relevant to PS3/BS3, but the reviewed evidence contains no variant-specific NF1 assay, transcript analysis, protein assay, cellular assay, animal model, or other validated functional result for NM_001042492.2:c.7584A>G (p.Gln2528=). The available literature either does not mention this variant or provides only gene-level biology and therefore cannot establish abnormal function for PS3.

Rule

Generic ACMG/AMP PS3 requires well-established functional studies showing a damaging effect; no variant-specific functional study is available. The NF1 specification was checked first but provides no PS3-specific rule.

Evidence considered

• The NF1 ClinGen specification record is present, but its extracted PS3/BS3 rule payload is empty and no criterion-specific calibration is supplied.
• The ACMG/AMP guideline states that assays assessing mRNA effects can be informative for coding-sequence variants, including effects on mRNA stability, processing, or translation; it reports no result for this variant.
• The variant is synonymous, NM_001042492.2:c.7584A>G (NP_001035957.1:p.(Gln2528=)), and the reviewed variant-specific literature extraction contains no functional assay or transcript result for it.

Still missing

• Variant-specific functional testing is unavailable, including transcript-level analysis, splicing assay, protein-function assay, or validated cellular/organismal assay.
• Assay controls, biological relevance, quantitative effect size, and calibration against established pathogenic and benign controls are unavailable.

Sources

Reasoning

PM6 cannot be assessed because the available case evidence does not document a presumed de novo occurrence without confirmed parental testing. There is no reported proband, parental, maternity, paternity, or family testing record for NM_001042492.2:c.7584A>G. The NF1-specific CSPEC is present but has no usable criterion-specific rule payload, so generic ACMG/AMP principles apply and do not permit presumed de novo evidence without a documented basis.

Evidence considered

• The case materials contain no documented parental testing, family pedigree, or presumed de novo report for this exact variant.
• The retrieved NF1 CSPEC does not provide a usable PM6-specific rule payload, so generic ACMG/AMP principles were used.
• The available paper extracts do not report this exact variant in a presumed de novo family observation.

Still missing

• A clinical report describing the proband and variant detection
• Evidence that both parents were tested or otherwise informative
• Maternity and paternity confirmation
• Documentation supporting presumed rather than confirmed de novo status

Sources

Reasoning

PP1 cannot be assessed because no affected relatives carrying the variant, informative meioses, pedigree structure, or segregation results are documented. The case evidence contains no family-level genotype-phenotype observations for NM_001042492.2:c.7584A>G, and the literature extracts do not identify this exact variant in a segregation study. The NF1-specific CSPEC is present but contains no usable criterion-specific rule payload, so no gene-specific segregation threshold can be applied.

Evidence considered

• The case materials provide no family pedigree, affected-relative testing, or informative meiosis count for this exact variant.
• No paper_extracts entry reports c.7584A>G or p.Gln2528= in a family segregation analysis.
• The retrieved NF1 CSPEC has no usable criterion-specific PP1 rule payload, so no gene-specific threshold is available.

Still missing

• Affected relatives with confirmed NF1 phenotype
• Genotypes for affected and unaffected relatives
• Number of informative meioses
• Pedigree and phenotype concordance details
• Independent segregation observations

Sources

Reasoning

No patient-level phenotype, diagnostic features, or disease-specific clinical presentation is supplied for this variant. Although NF1 is the relevant disease context, gene-level disease descriptions cannot establish that this exact variant occurs in an individual with a highly specific phenotype. PP4 cannot be assessed without documented phenotype and diagnostic specificity.

Rule

Generic PP4: patient phenotype or family history is highly specific for a disease with a single-gene etiology; patient-level phenotype evidence is required.

Still missing

• Patient-level phenotype and diagnostic features are not available.

Reasoning

The NF1 ClinGen specification record is present but contains no BS3-specific rules. Generic ACMG/AMP guidance recognizes well-established functional assays as relevant to BS3, but the reviewed evidence contains no variant-specific NF1 assay demonstrating normal function, normal transcript processing, preserved protein activity, or an appropriately controlled benign cellular or organismal phenotype for NM_001042492.2:c.7584A>G (p.Gln2528=). Absence of a functional result cannot be converted into benign functional evidence.

Rule

Generic ACMG/AMP BS3 requires well-established functional studies showing no damaging effect; no variant-specific functional study is available. The NF1 specification was checked first but provides no BS3-specific rule.

Evidence considered

• The NF1 ClinGen specification record is present, but its extracted PS3/BS3 rule payload is empty and no criterion-specific calibration is supplied.
• The ACMG/AMP guideline describes functional assays as potentially informative for PS3/BS3, including mRNA effects, but reports no normal-function result for this variant.
• The reviewed variant-specific literature extraction contains no controlled assay demonstrating normal NF1 transcript or protein function for c.7584A>G (p.Gln2528=).

Still missing

• Variant-specific functional testing is unavailable, including transcript-level analysis, splicing assay, protein-function assay, or validated cellular/organismal assay demonstrating a normal result.
• Assay controls, biological relevance, quantitative effect size, and calibration against established pathogenic and benign controls are unavailable.

Sources

Reasoning

BS4 cannot be assessed because the available case evidence does not document unaffected relatives who carry the variant despite an adequately informative phenotype assessment. The presence of the variant in population databases is not family non-segregation evidence, and no affected/unaffected relative genotypes or phenotype evaluations are reported for NM_001042492.2:c.7584A>G. The NF1-specific CSPEC is present but contains no usable criterion-specific rule payload, so no gene-specific BS4 rule changes this conclusion.

Evidence considered

• The case materials contain no unaffected relative genotype-phenotype observations for this exact variant.
• Population observations in gnomAD do not establish family non-segregation and were not used for BS4.
• The retrieved NF1 CSPEC has no usable criterion-specific BS4 rule payload, so generic ACMG/AMP principles were applied.

Still missing

• Unaffected relatives with reliable NF1 phenotype assessment
• Confirmed variant genotypes in those relatives
• Age and clinical evaluation sufficient to classify relatives as unaffected
• Pedigree context demonstrating informative non-segregation

Sources

Reasoning

BP2 requires a documented observation of the variant in trans with a pathogenic variant in an affected individual for a dominant condition, or in cis with a pathogenic variant for any condition. The available case evidence contains no affected-proband genotype, second pathogenic variant, or reliable cis/trans phase information for NM_001042492.2:c.7584A>G. Therefore BP2 cannot be assessed.

Rule

For an autosomal-dominant condition, BP2 requires the variant to be observed in trans with a pathogenic variant in an affected individual; phase and affected-proband evidence are required.

Evidence considered

• The NF1 framework specifies autosomal dominant inheritance, making a documented affected individual with a pathogenic variant in trans the relevant BP2 configuration.
• The available evidence does not document an affected proband, a second pathogenic or likely pathogenic variant, or cis/trans phase for NM_001042492.2:c.7584A>G.

Still missing

• Affected-proband genotype data are unavailable.
• No second pathogenic or likely pathogenic variant is documented for phase comparison.
• Cis/trans phase has not been established.

Sources

Reasoning

No documented patient case demonstrates a well-established alternative molecular diagnosis that explains the relevant phenotype while this exact NF1 variant is present. The available ClinVar benign laboratory assertions are not BP5 evidence, and no applicable NF1-specific BP5 rule or numeric likelihood-ratio threshold is available. BP5 therefore cannot be assessed from the supplied evidence.

Rule

Generic BP5: a pathogenic variant in an alternative gene explains the patient's phenotype, making the evaluated variant unlikely to explain it; no qualifying case evidence is available.

Still missing

• A documented alternative pathogenic diagnosis in an affected individual is not available.