FGFR1 c.1746C>A, p.(Cys582Ter)

Reasoning

NM_001174067.1:c.1746C>A creates a nonsense change, p.(Cys582Ter) (NP_001167538.1, 854 aa reference protein per Mutalyzer/VariantValidator prefetch data). No official CSPEC/VCEP framework is available for FGFR1, so the generic ClinGen SVI PVS1 decision tree (PMC6185798) applies. Gene-level context supports an eligible LOF disease mechanism: targeted germline literature review found FGFR1-related Hartsfield syndrome (haploinsufficiency/LOF-associated developmental disorder) with no evidence contradicting LOF as a valid mechanism. Transcript-level analysis: the PTC falls in exon 13 of 18 coding exons (VariantValidator exonic position mapping, both GRCh37 and GRCh38), far upstream of the final exon-exon junction (exon 17/18 boundary) and well beyond the 50 bp NMD-escape window, so the transcript is predicted to undergo nonsense-mediated decay. Even if NMD were incomplete, the predicted truncated protein (582 of 854 residues, ~32% of the C-terminus lost) would eliminate the bulk of the tyrosine kinase domain and the entire C-terminal tail: reference protein positions 581-854 encode 'RWELPRDRLVLGKPLGEGCFGQVVLAEAIGL...' (the start of the kinase domain and its catalytic core/activation loop), while the predicted truncated protein terminates immediately after '...KNIINLLGA*', removing essentially the entire kinase catalytic domain. This is a biologically critical, non-dispensable region (the kinase domain is required for FGFR1 signal transduction), and there is no evidence of exon skipping, alternative rescue transcript, or population-level enrichment of LoF variants in this exon that would argue against pathogenic impact. All generic PVS1 downgrade considerations flagged by the pipeline (transcript relevance, NMD status, exon biological importance) were evaluated and none support a downgrade.

Rule

PVS1

Evidence considered

• pvs1_gene_context.json: targeted germline literature review found FGFR1 loss-of-function is a supported disease mechanism (FGFR1-Related Hartsfield Syndrome), gating generic PVS1 framework eligibility (pvs1_gene_gate: eligible).
• pvs1_variant_assessment.json: classifies the variant as a nonsense/consequence_class 'nonsense' change, applies the generic PVS1 framework (framework_cite: pvs1_generic_framework, PMC6185798), with suggested_default_strength PVS1 pending confirmation of transcript relevance, NMD status, and exon importance.
• Mutalyzer/VariantValidator prefetch normalization data: protein consequence NP_001167538.1:p.(Cys582Ter); reference protein length 854 aa (position_last_original: 854); PTC at residue 582 (position_last_predicted: 582); VariantValidator variant_exonic_positions place the variant in exon 13 (both GRCh37 NC_000008.10 and GRCh38 NC_000008.11), well upstream of the terminal exon 18, supporting NMD prediction per the >50bp/not-last-exon rule.
• Reference protein sequence flanking the truncation (residues 581-854) shows the truncated region begins 'RWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYCYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQEYLDLSMPLDQYSPSFPDTRSSTCSSGEDSVFSHEPLPEEPCLPRHPAQLANGGLKRR*', i.e. essentially the entire tyrosine kinase catalytic domain and C-terminal tail, confirming the truncation removes a functionally critical region even if NMD were incomplete.

Still missing

• No official CSPEC/VCEP-specific PVS1 decision tree exists for FGFR1; generic ClinGen SVI PVS1 framework was used by necessity.
• No gnomAD-based population constraint or exon-level LoF enrichment data specific to exon 13 was available to further corroborate that this exon is not tolerant of truncation.

Sources

Reasoning

The exact variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. With no FGFR1-specific population specification available, this fulfills generic ACMG/AMP PM2 at supporting strength: absence from population databases, or occurrence at an extremely low frequency if observed, for a variant assessed in a rare-disease context.

Rule

Generic ACMG/AMP PM2, supporting strength: absent from controls (or extremely low frequency if present) in population databases for a rare disorder.

Evidence considered

• The normalized GRCh37 allele 8-38274834-G-T is absent from gnomAD v2.1.
• The normalized GRCh38 allele chr8-38417316-G-T is absent from gnomAD v4.1 and gnomAD-Canada v1.0.
• No FGFR1 VCEP/ClinGen gene-specific population-frequency specification was retrieved; generic ACMG/AMP population evidence is therefore used.

Still missing

• The bundle does not provide cohort allele-number denominators or ancestry-stratified callable counts; this does not negate the consistently reported absence but limits quantitative maximum credible allele-frequency analysis.

Sources

Reasoning

No gene-specific CSPEC/VCEP PP3/BP4 lookup material is available for FGFR1 (generic ACMG fallback framework in use). SpliceAI/Pangolin scoring for NM_001174067.1:c.1746C>A shows no predicted splice impact (max delta score = 0.00; SG = 0.005, SL = -0.141), well below the calibrated damaging-splicing threshold established by the SpliceAI validation study (Jaganathan et al. 2019, PMID 30661751). This is a computational line of evidence (splice-impact prediction) indicating no impact on splicing for this variant, supporting BP4 at supporting strength for the splicing subpath. The missense meta-predictor path (BayesDel/REVEL) is not applicable since this is a nonsense (stop-gain) variant, and BayesDel is excluded from consideration per this pipeline's calibration policy regardless of its numeric value, so BP4 here rests solely on the SpliceAI negative splicing prediction rather than convergent missense evidence.

Rule

Generic ACMG/AMP BP4 (computational evidence suggests no impact on gene/gene product)

Evidence considered

• SpliceAI/Pangolin lookup (spliceai source) shows max delta score = 0.00 (pangolin_SG = 0.005, pangolin_SL = -0.141) for NM_001174067.1:c.1746C>A, indicating no predicted splice-altering effect.
• SpliceAI's calibrated delta-score framework (Jaganathan et al. 2019, PMID 30661751) supports treating scores at or near 0.00 as evidence against a splice-altering effect.
• This is a nonsense (stop-gain) variant (NP_001167538.1:p.(Cys582Ter)) located mid-exon (exon boundaries c.1701-1846 per selector data), not at a canonical splice site, consistent with the null SpliceAI prediction.

Still missing

• Only a single computational tool (SpliceAI/Pangolin) was available for the splice-impact assessment; no second independent splice predictor was available to corroborate the null-impact call.
• No gene-specific FGFR1 VCEP PP3/BP4 lookup table was available to check for a pre-assigned code.

Sources

Reasoning

No gene-specific CSPEC/VCEP PP3/BP4 lookup material is available for FGFR1 in this case (vcep_materials.json: 'no cspec url available'; case_summary.json framework_mode = generic_acmg), so generic ACMG in-silico criteria apply. The variant NM_001174067.1:c.1746C>A produces a stop-gain (NP_001167538.1:p.(Cys582Ter)), not a missense or synonymous change, so the missense meta-predictor path (BayesDel/REVEL/aGVGD) is not the relevant computational domain here; only splice-impact prediction is applicable. SpliceAI/Pangolin scoring shows no significant predicted splice impact (max delta score = 0.00; pangolin_SG = 0.005, pangolin_SL = -0.141), which does not meet any calibrated threshold for a damaging splicing prediction. REVEL was not found for this variant (evidence.json: revel.found = false) and BayesDel, although scored (0.66), has no verified published calibration threshold available to this pipeline and per instruction must be treated as not_available for PP3/BP4 regardless of the numeric value. There is therefore no computational evidence of a damaging effect on gene/gene product supporting PP3.

Rule

Generic ACMG/AMP PP3 (computational evidence supports a deleterious effect)

Evidence considered

• SpliceAI/Pangolin lookup (spliceai source) shows max delta score = 0.00 (pangolin_SG = 0.005, pangolin_SL = -0.141) for NM_001174067.1:c.1746C>A, indicating no predicted splice-altering effect.
• SpliceAI's calibrated donor/acceptor delta-score framework (Jaganathan et al. 2019, PMID 30661751) treats delta scores well below 0.2 as not supportive of a splice-altering effect; this variant's score of 0.00 falls far under that threshold.
• Variant is a nonsense (stop-gain) substitution (NP_001167538.1:p.(Cys582Ter)), not missense or synonymous, so the BayesDel/REVEL missense in-silico path is not the applicable evidence domain for this variant; only the splice-prediction path is relevant.
• BayesDel score of 0.66 was retrieved locally (source_registry key 'bayesdel') but is treated as insufficiently calibrated for PP3/BP4 per this pipeline's rule that no verified published BayesDel threshold/publication is available; therefore it cannot be used to support PP3.

Still missing

• No gene-specific FGFR1 VCEP PP3/BP4 lookup table was available to check for a pre-assigned code.
• REVEL score not found/available for this variant.
• BayesDel score exists (0.66) but lacks a verified published calibration threshold citable by this pipeline, so it cannot be used for PP3.

Sources

Reasoning

PP5 is not met because ClinVar returned no exact-variant record for FGFR1 c.1746C>A (p.Cys582Ter), and therefore no exact-variant Pathogenic/Likely pathogenic expert-panel assertion exists.

Rule

Apply PP5 only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; do not use laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• The exact-variant ClinVar query returned no result; no ClinVar submissions or expert-panel classification were present.

Sources

Reasoning

No allele frequency is reported because the variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Therefore, the stand-alone benign BA1 population-frequency criterion is not met.

Rule

Generic ACMG/AMP BA1: allele frequency must be sufficiently high for stand-alone benign evidence.

Evidence considered

• The exact GRCh37 allele 8-38274834-G-T was absent from gnomAD v2.1.
• The exact GRCh38 allele chr8-38417316-G-T was absent from gnomAD v4.1 and gnomAD-Canada v1.0.
• No population frequency approaches a BA1 threshold; ancestry-specific frequency and homozygote counts are consequently zero/not reported rather than evidence of benignity.

Sources

Reasoning

The variant is absent from the available gnomAD datasets, so there is no allele frequency greater than expected for an FGFR1-associated disorder. BS1 is not met.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder.

Evidence considered

• The queried allele was absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• Because no allele count, frequency, ancestry enrichment, or homozygote count is reported, population data do not support a benign strong frequency criterion.

Sources

Reasoning

BP6 is not met because ClinVar returned no exact-variant record for FGFR1 c.1746C>A (p.Cys582Ter), and therefore no exact-variant Benign/Likely benign expert-panel assertion exists.

Rule

Apply BP6 only to an exact-variant ClinVar expert-panel Benign or Likely benign classification; do not use laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• The exact-variant ClinVar query returned no result; no ClinVar submissions or expert-panel classification were present.

Sources

Reasoning

The case-evidence bundle contains no proband phenotype, parental genotypes, parentage confirmation, or familial testing for FGFR1 c.1746C>A (p.Cys582Ter); confirmed de novo occurrence cannot be assessed.

Rule

Generic ACMG/AMP de novo evidence: PS2 requires a confirmed de novo occurrence in a patient with a phenotype consistent with the gene-associated disorder.

Evidence considered

• The retrieved framework states that no FGFR1 CSPEC/VCEP specification or local gene-specific framework is available and that generic ACMG/AMP fallback applies.
• The consolidated bundle includes variant normalization and population/database evidence only; it provides no individual-level parental, phenotype, or segregation data.

Still missing

• Obtain the proband's phenotype and molecular result.
• Obtain testing of both biological parents for the exact variant, including method and parental identity confirmation where available.
• Document whether the proband phenotype is consistent with an established FGFR1-related disorder.

Sources

Reasoning

No CSPEC/VCEP functional assay framework is available for FGFR1 in this case (cspec.found=false), and the case-evidence bundle contains no functional/biochemical assay data (e.g., kinase activity, receptor signaling, cell proliferation, or NMD/expression assays) for NM_001174067.1:c.1746C>A (p.Cys582Ter). No PMIDs specific to functional characterization of this variant were retrieved by the literature search; the retrieved PVS1-support papers address germline disease association/mechanism, not a validated functional assay of this specific variant.

Still missing

• No validated functional/biochemical assay data available for this specific variant
• No VCEP-specific PS3 assay framework for FGFR1 to calibrate strength
• No literature identified describing an experimental assay of p.Cys582Ter

Reasoning

No variant-specific affected-case series, control data, or case-control enrichment analysis was retrieved for FGFR1 c.1746C>A (p.Cys582Ter); PS4 cannot be assessed.

Rule

Generic ACMG/AMP PS4: require statistically supported increased prevalence in affected individuals compared with controls.

Evidence considered

• The consolidated literature pass contains no PMIDs or variant-specific publications for this variant.
• No FGFR1 VCEP/ClinGen CSPEC or local gene-specific framework was retrieved; generic ACMG/AMP is the applicable fallback.

Still missing

• Variant-specific affected and control counts, with phenotype definition and ascertainment information, are needed to evaluate case-control enrichment.

Reasoning

No affected-proband observation of NM_001174067.1:c.1746C>A with a pathogenic/likely pathogenic FGFR1 variant, and no phase result establishing trans configuration, is available. PM3 cannot be assessed.

Rule

Generic ACMG/AMP PM3: in a recessive disorder, the variant is detected in trans with a pathogenic variant.

Evidence considered

• The consolidated case-evidence bundle reports no FGFR1 CSPEC/VCEP framework and identifies generic ACMG/AMP fallback.
• The bundle contains no affected-proband, second-variant, parental/segregation, or phase evidence for this variant.

Still missing

• Affected-proband genotype data identifying any second FGFR1 pathogenic/likely pathogenic variant.
• Phase evidence demonstrating whether the variants are in trans.
• Phenotype and inheritance information sufficient to establish that the observed disease presentation is consistent with an FGFR1 recessive disorder.

Sources

Reasoning

No case report or testing record establishes that FGFR1 c.1746C>A (p.Cys582Ter) occurred de novo with untested or incompletely tested parents; PM6 cannot be assessed.

Rule

Generic ACMG/AMP de novo evidence: PM6 may be considered only for an assumed de novo occurrence in an affected individual when parental confirmation is unavailable or incomplete.

Evidence considered

• The retrieved framework states that no FGFR1 CSPEC/VCEP specification or local gene-specific framework is available and that generic ACMG/AMP fallback applies.
• The consolidated bundle provides no proband-level report and no parental testing information for this variant.

Still missing

• Obtain the proband's phenotype and molecular result.
• Obtain parental testing status and results for the exact variant; if one or both parents remain unavailable, document the basis for an assumed de novo occurrence.

Sources

Reasoning

No family pedigree, relative genotypes, affected-status data, or informative meioses are provided for FGFR1 c.1746C>A (p.Cys582Ter); co-segregation cannot be assessed.

Rule

Generic ACMG/AMP PP1 requires co-segregation of the variant with disease in affected family members; no gene-specific segregation threshold was retrieved.

Evidence considered

• The retrieved framework states that no FGFR1 CSPEC/VCEP specification or local gene-specific framework is available and that generic ACMG/AMP fallback applies.
• The consolidated bundle contains no pedigree, familial genotype, phenotype, or meiosis information.

Still missing

• Obtain a pedigree with phenotypes and genotypes for informative relatives.
• Document the number of informative segregations/meioses and the testing method for the exact variant.

Sources

Reasoning

No proband phenotype, diagnostic workup, or phenotype-specificity evidence was provided for this variant; PP4 cannot be assessed.

Rule

Generic ACMG/AMP PP4: the patient's phenotype or family history must be highly specific for a disease with a single genetic etiology.

Evidence considered

• The case bundle identifies FGFR1 but contains no patient-level phenotype or diagnostic evaluation for the individual carrying c.1746C>A.
• No FGFR1 VCEP/ClinGen CSPEC or local gene-specific framework was retrieved; generic ACMG/AMP is the applicable fallback.

Still missing

• Provide the individual's phenotype, relevant negative findings, and differential diagnosis/genetic testing results to determine whether the presentation is highly specific for an FGFR1-related disorder.

Reasoning

BS2 requires observation in healthy adult individual(s) for a disorder expected to be fully penetrant at an early age. The available population sources report no observations of this allele and provide no phenotype-linked healthy-adult carrier evidence; BS2 cannot be assessed.

Rule

Generic ACMG/AMP BS2: observed in a healthy adult individual for a fully penetrant early-onset disorder.

Evidence considered

• gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 each report the queried allele as absent, so they contain no carrier or homozygote observations to evaluate against BS2.
• No source in the case bundle establishes that the relevant FGFR1-associated disorder is fully penetrant with early onset, nor does it link population participants to unaffected adult status.

Still missing

• Phenotype- and age-annotated observations of carriers are unavailable.
• Disease-specific penetrance and age-of-onset information sufficient to establish the BS2 prerequisite are unavailable in the case evidence.

Sources

Reasoning

No CSPEC/VCEP functional assay framework is available for FGFR1 in this case (cspec.found=false), and the case-evidence bundle contains no functional/biochemical assay data showing normal/benign function for NM_001174067.1:c.1746C>A (p.Cys582Ter). No PMIDs specific to functional characterization of this variant were retrieved.

Still missing

• No validated functional/biochemical assay data showing normal function for this specific variant
• No VCEP-specific BS3 assay framework for FGFR1 to calibrate strength
• No literature identified describing an experimental assay of p.Cys582Ter

Reasoning

No informative relatives with confirmed phenotype and genotype are reported, so lack of segregation between FGFR1 c.1746C>A (p.Cys582Ter) and disease cannot be assessed.

Rule

Generic ACMG/AMP BS4 requires convincing lack of segregation with disease in affected family members; no gene-specific non-segregation specification was retrieved.

Evidence considered

• The retrieved framework states that no FGFR1 CSPEC/VCEP specification or local gene-specific framework is available and that generic ACMG/AMP fallback applies.
• The consolidated bundle contains no familial genotype/phenotype data from which non-segregation could be demonstrated.

Still missing

• Obtain pedigree-based genotype and phenotype data from informative affected and unaffected relatives.
• Assess age-dependent expression, penetrance, and phenocopy considerations before interpreting any observed non-segregation.

Sources

Reasoning

There is no observation of NM_001174067.1:c.1746C>A with a pathogenic/likely pathogenic FGFR1 variant in cis, nor an observation in trans in a setting where that configuration would support BP2. BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2: the variant is 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.

Evidence considered

• The consolidated case-evidence bundle reports no FGFR1 CSPEC/VCEP framework and identifies generic ACMG/AMP fallback.
• The bundle contains no co-occurrence, phase, or inheritance data for this variant.

Still missing

• Affected-proband or other individual genotype data identifying any co-occurring FGFR1 pathogenic/likely pathogenic variant.
• Phase evidence establishing cis or trans configuration of any co-occurring FGFR1 variants.
• Disease-specific inheritance and penetrance context for any proposed trans observation in a dominant FGFR1 disorder.

Sources

Reasoning

No proband-level evidence of an independent molecular diagnosis that fully explains the reported phenotype was provided; BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5: evaluate only when a variant is found in a case with an alternate molecular basis for disease.

Evidence considered

• The case bundle contains no patient-level phenotype or alternate molecular diagnosis.

Still missing

• Provide phenotype information and results of comprehensive genetic testing to determine whether an alternate molecular diagnosis fully explains the presentation.