FGFR1 c.1638C>A, p.Asn546Lys

Reasoning

PM2 is met at supporting strength. NM_023110.3:c.1638C>A (FGFR1 p.Asn546Lys) is reported as absent from gnomAD v2.1 exomes and gnomAD v4.1 exomes, and the non-cancer subsets are also reported as absent (v2.1 non-cancer exomes and v3.1 non-cancer genomes). This is below the supplied generic PM2 supporting threshold of <=0.0001; no population allele count, homozygote, or ancestry-specific frequency is available.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 exomes report the exact variant as absent.
• gnomAD v4.1 exomes report the exact variant as absent.
• The evidence also reports absence from the gnomAD v2.1 non-cancer exome subset and the gnomAD v3.1 non-cancer genome subset; no governing VCEP specification requires these subsets because no VCEP covers FGFR1 in this case.
• The generic PM2 calibration supplied for this case is <=0.0001 for supporting strength, based on the ClinGen SVI recommendation cited in the prompt and ACMG/AMP 2015 (PMID:25741868); absence is below this threshold.

Sources

Reasoning

The variant is a missense substitution, NM_023110.3:c.1638C>A (p.Asn546Lys), so the generic PP3/BP4 missense path is REVEL only; SpliceAI is not used for this path. The REVEL score is 0.646, meeting the published generic PP3 supporting threshold of >=0.644 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• NM_023110.3:c.1638C>A is a missense variant producing p.Asn546Lys, selecting the REVEL-only computational path; SpliceAI is not counted.
• Local REVEL predictor lookup reports a score of 0.646 (source_registry key: revel).
• The generic PP3 supporting threshold is REVEL >=0.644, using the supplied ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet; PMID:36413997).
• BayesDel score -0.0722477 is not used because no generic ACMG-strength calibration is established.

Sources

Reasoning

The exact variant is reported as pathogenic or likely pathogenic by ordinary ClinVar submissions, but the ClinVar audit records zero expert-panel submissions. The available records are clinical-laboratory, research, OMIM/literature-only, or other non-expert assertions; therefore they do not satisfy the required exact-variant reputable expert-panel source condition for PP5.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 224896 is an exact match for NM_023110.3:c.1638C>A (p.Asn546Lys), but the submission audit records expert_panel_submissions = 0.
• The pathogenic and likely pathogenic assertions are from ordinary laboratory, research, OMIM/literature-only, or other non-expert submissions and are not used to trigger PP5.

Sources

Reasoning

BA1 is not met. NM_023110.3:c.1638C>A (FGFR1 p.Asn546Lys) was absent from gnomAD v2.1 and gnomAD v4.1, so no allele-frequency value reaches the generic stand-alone benign threshold of 0.05. No popmax point estimate or grpmax FAF is available, and the variant's pathogenic ClinVar consensus further provides no basis for applying BA1 from an unverified frequency.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 (exome) reports the exact variant as absent; no AC, AN, AF, popmax AF, or grpmax FAF is available.
• gnomAD v4.1 (exome) reports the exact variant as absent; no AC, AN, AF, popmax AF, or grpmax FAF is available.
• The generic BA1 calibration supplied for this case is >=0.05, from ACMG/AMP 2015 (PMID:25741868); no qualifying frequency is present.
• ClinVar reports the exact variant as Pathogenic with multiple submitters and no conflicts, so a stand-alone benign BA1 call would require verified high-frequency evidence rather than a default assumption.

Sources

Reasoning

BS1 is not met on the available population data. The exact variant is absent from gnomAD v2.1 and v4.1, with no filtering allele frequency, popmax point estimate, or ancestry-specific observation to compare with the disorder's expected frequency. Therefore the generic BS1 default threshold of >=0.01 is not reached; no maximum-credible-frequency calculation is needed because there is no observed frequency requiring interpretation.

Rule

Allele frequency is greater than expected for disorder.

Evidence considered

• gnomAD v2.1 (exome) reports the exact variant as absent, with no grpmax FAF or popmax value.
• gnomAD v4.1 (exome) reports the exact variant as absent, with no grpmax FAF or popmax value.
• The generic BS1 calibration supplied for this case is >=0.01; it is not reached. The supplied guidance identifies Whiffin et al. 2017 (PMID:28518168) as the maximum-credible-frequency reference, but a calculation is unnecessary when no population frequency is observed.

Sources

Reasoning

The variant is a missense substitution, so the generic PP3/BP4 missense path is REVEL only; the SpliceAI result is not evidence for BP4 in this situation. The REVEL score is 0.646, which does not meet the strongest, moderate, or supporting BP4 thresholds of <=0.016, <=0.183, or <=0.29, respectively, under the supplied ClinGen SVI calibration (Pejaver et al. 2022, PMID:36413997). BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)

Evidence considered

• NM_023110.3:c.1638C>A is a missense variant, selecting the REVEL-only computational path; SpliceAI is not counted for BP4.
• Local REVEL predictor lookup reports a score of 0.646 (source_registry key: revel).
• The supplied generic BP4 thresholds are REVEL <=0.016 (strong), <=0.183 (moderate), and <=0.29 (supporting), using the ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet; PMID:36413997); 0.646 meets none of them.
• BayesDel score -0.0722477 is not used because no generic ACMG-strength calibration is established.

Sources

Reasoning

No exact-variant ClinVar expert-panel classification of benign or likely benign was identified. ClinVar contains pathogenic or likely pathogenic ordinary submissions and no expert-panel submissions; those records cannot trigger BP6.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 224896 is an exact match, but the submission audit records zero expert-panel submissions and no benign or likely benign expert-panel classification.
• Ordinary laboratory submissions, aggregate labels, and non-expert assertions were excluded from BP6.

Sources

Reasoning

The variant is NP_075598.2:p.(Asn546Lys). Literature reports the same amino-acid substitution as FGFR1 N544K under an alternate two-residue numbering convention, and another study reports p.N546K, but the available evidence does not establish a previously pathogenic variant caused by a different nucleotide change at this codon. The exact ClinVar record for c.1638C>A cannot independently satisfy PS1 because it is the variant under review. No qualifying independent same-amino-acid, different-nucleotide pathogenic comparator was identified.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• The target variant is NM_023110.3:c.1638C>A, NP_075598.2:p.(Asn546Lys).
• PMID:26810070 reports FGFR1 N544K in LGNT34; the case materials specify that this corresponds to precursor-protein p.(N546K) under a two-residue numbering offset, not a different nucleotide change at the codon.
• PMID:31250151 reports FGFR1 p.N546K in 22 of 30 tumors, but does not establish an independent pathogenic nucleotide change for PS1.
• ClinVar variation 224896 is the exact c.1638C>A (p.Asn546Lys) record and therefore was not treated as an independent PS1 comparator.

Still missing

• A previously established pathogenic FGFR1 nucleotide change producing p.Asn546Lys at the same codon is needed.

Sources

Reasoning

The available evidence does not document a proband with confirmed clinical disease who carries NM_023110.3:c.1638C>A as a de novo variant. No parental testing results are provided, and there is no confirmation of both maternity and paternity or documentation of no family history. The reviewed variant-specific tumor studies describe FGFR1 p.N546K/N544K in tumor cohorts, not a germline trio or family study.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• PMID:31250151 reports FGFR1 p.N546K in 22 of 30 molecularly defined rosette-forming glioneuronal tumors and explicitly provides no segregation data or parental testing.
• PMID:26810070 reports an FGFR1 N544K tumor finding corresponding to the precursor-protein p.(N546K) notation under the case's numbering offset; it provides no parental testing or family-history evidence.
• No case-level trio, maternity, paternity, or family-history evidence is present in the available records.

Still missing

• A clinically characterized proband with the relevant disease must be identified.
• Variant testing in both biological parents is required to confirm maternity and paternity and establish de novo status.
• Family history and possible mosaic or non-germline origin require documentation.

Sources

Reasoning

The available variant-specific literature reports FGFR1 p.N546K/p.N544K in tumors and describes it as activating, but the reviewed extracts provide no variant-specific in vitro or in vivo functional assay results, assay controls, validation, reproducibility, or robustness information. The evidence therefore does not establish the well-established functional-study standard required for PS3, and no strength can be calibrated.

Rule

PS3: Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• PMID:31250151, Results subsection ‘RGNTs are characterized by alterations affecting MAPK and PI3K signaling pathways,’ paragraph 1 and Supplementary Table 2: FGFR1 p.N546K was found in 22 of 30 tumors and described as an activating kinase-domain alteration, but no variant-specific functional assay was reported in the extracted evidence.
• PMID:26810070, Results subsection ‘FGFR1 alterations in cerebral LGNTs with oligodendroglial phenotype’: an FGFR1 N544K mutation was reported in tumor LGNT34, corresponding to the case variant under the supplied numbering relationship, but no variant-specific functional assay was reported in the extracted evidence.

Still missing

• A variant-specific in vitro or in vivo assay demonstrating a damaging effect is needed.
• Assay controls, biological relevance, validation, reproducibility, and robustness are not documented.

Sources

Reasoning

No case-control comparison meeting the generic PS4 definition was available. The reviewed variant-specific papers report FGFR1 p.(N546K) in affected tumor cohorts, including 22 of 30 rosette-forming glioneuronal tumors in PMID:31250151 and one tumor in PMID:26810070, but provide no unaffected/population control count, matched-ancestry control frequency, odds ratio, relative risk, or confidence interval. Therefore an OR/CI comparison cannot be computed and the criterion is not assessed. The literature_pass.json ai_classified_papers array is empty, so there were no pre-classified PS4 papers requiring additional classifier verification.

Rule

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.

Evidence considered

• PMID:31250151, Results and Supplementary Table 2: the exact protein change p.N546K was found in 22 of 30 molecularly defined rosette-forming glioneuronal tumors; no unaffected or population control comparison was reported.
• PMID:26810070, Results: the corresponding FGFR1 N544K/p.(N546K) change was reported in tumor LGNT34 within a 91-tumor cohort; no control comparison or case-control frequency was reported.
• gnomAD v2.1 and gnomAD v4.1 report the variant as absent, but no affected-case denominator or matched-ancestry control frequency suitable for a PS4 OR/CI calculation is supplied.
• The literature_pass.json ai_classified_papers array is empty; no classifier-read PS4 papers were available for verification.

Still missing

• A case-control dataset or matched-ancestry control frequency for NM_023110.3:c.1638C>A is needed.
• An odds ratio or relative risk with a 95% confidence interval cannot be derived from the available reports.

Sources

Reasoning

p.Asn546Lys lies in the FGFR1 kinase domain, and PMID:31250151 describes p.N546K as an activating alteration within that domain; PMID:26810070 reports the corresponding N544K as an FGFR1 hotspot mutation. However, generic PM1 also requires the hotspot or critical domain to be without benign variation, and the supplied evidence does not provide a domain-wide benign-variation analysis or an established benign-variation exclusion. The cancer-hotspot search returned no statistically significant hotspot row, so that source does not independently close the gap.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• PMID:31250151 states that FGFR1 p.N546K is an activating missense alteration within the kinase domain; the study found it in 22 of 30 rosette-forming glioneuronal tumors.
• PMID:26810070 reports the corresponding FGFR1 N544K in LGNT34 and describes FGFR1 hotspot mutations in its tumor cohort.
• The Cancer Hotspots query for FGFR1 N546 returned no result and cannot establish a hotspot route.
• No VCEP domain_tables entry exists for FGFR1; generic PM1 therefore applies, but the supplied evidence does not establish the required absence of benign variation.

Still missing

• Evidence that the relevant FGFR1 kinase-domain or hotspot region lacks benign variation is needed.

Sources

Reasoning

PM3 is not assessed. The governing rule applies to recessive disorders and requires the variant to be detected in trans with a pathogenic variant. The available variant-specific report is a tumor study: FGFR1 N544K, corresponding to NP_075598.2:p.(N546K) for this case, was reported with R659L on different alleles in one tumor (PMID:26810070). However, the evidence does not establish that this observation represents a recessive disorder, does not document an affected proband with a recessive FGFR1 phenotype, and does not establish R659L as pathogenic under the supplied evidence. Parental or offspring testing and clinically relevant inheritance information are not available.

Rule

For recessive disorders, detected in trans with a pathogenic variant

Evidence considered

• Genetic alterations in uncommon low-grade neuroepithelial tumors, Results: in tumor LGNT34, two FGFR1 mutations, N544K and R659L, were identified on different alleles; N544K corresponds to the case variant p.(N546K) under the transcript numbering used here.
• This tumor sequencing observation does not by itself establish a recessive clinical disorder, affected-proband inheritance, or pathogenicity of the R659L partner variant.

Still missing

• A clinically relevant recessive FGFR1 disorder must be established for this observation.
• The partner R659L variant must be independently established as pathogenic.
• Parental, offspring, or other validated phase testing and affected-proband context are needed.

Sources

Reasoning

The available same-residue evidence reports p.N546K itself, including the alternate numbering N544K, rather than a different missense substitution at residue 546 that has been determined pathogenic. The collected PM5 candidate artifact contains no confirmed same-residue comparator. Therefore, the required pathogenic different-missense comparator has not been established.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The target residue is FGFR1 Asn546.
• The PM5 candidate summary reports zero same-residue candidates and no confirmed comparator.
• PMID:26810070 reports N544K, which is the same amino-acid change under the case's numbering offset, not a different missense change at the residue.
• PMID:31250151 reports p.N546K, also the target amino-acid change, not an alternate residue substitution.

Still missing

• A pathogenic FGFR1 missense variant changing Asn546 to an amino acid other than Lys is needed.

Sources

Reasoning

The available evidence does not document an assumed de novo occurrence of NM_023110.3:c.1638C>A in a clinically characterized patient. No parental testing, family-history assessment, or case-level inheritance information is provided. The reviewed publications describe somatic tumor occurrences of the p.N546K/N544K alteration rather than an assumed de novo germline event.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• PMID:31250151 reports p.N546K in tumor samples but does not report a de novo germline occurrence, parental testing, or segregation.
• PMID:26810070 reports a corresponding FGFR1 N544K tumor finding but does not provide inheritance or parental data.
• No case-level assumed-de-novo evidence is present in the available records.

Still missing

• A clinically characterized patient carrying the variant must be documented.
• Evidence suggesting de novo occurrence is required even if parental maternity and paternity are unconfirmed.
• Family-history and inheritance information are absent.

Sources

Reasoning

No affected relatives carrying NM_023110.3:c.1638C>A are reported, and no pedigree, number of informative meioses, or segregation analysis is available. The reviewed publications concern isolated tumor observations and do not establish co-segregation with disease in affected family members.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• PMID:31250151 describes p.N546K in a tumor cohort and reports no family segregation or affected relatives.
• PMID:26810070 describes an FGFR1 N544K tumor finding and reports no pedigree, affected-relative testing, or informative meioses.
• No familial co-segregation data are present in the available records.

Still missing

• A pedigree with clinically assessed affected relatives is required.
• Variant status in affected relatives and the number of informative meioses must be documented.
• The disease-gene relationship for the specific familial phenotype must be established in the evaluated family.

Sources

Reasoning

The target is a missense variant, but the supplied evidence does not establish both gene-level prerequisites for PP2: a low rate of benign missense variation and missense variants as a common disease mechanism for FGFR1. Recurrent activating FGFR1 missense variants are reported in tumor cohorts, but those observations alone do not provide the required gene-wide benign-missense rate or disease-mechanism assessment under generic PP2.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The variant consequence is missense: p.Asn546Lys.
• PMID:31250151 and PMID:26810070 describe recurrent activating FGFR1 missense alterations in tumor cohorts, but neither supplies the gene-wide benign-missense rate required for PP2.

Still missing

• A gene-level benign-missense constraint assessment and evidence that missense variants are a common FGFR1 disease mechanism are needed.

Sources

Reasoning

The available case materials do not provide the patient's phenotype or family history. Disease descriptions in publications and ClinVar condition labels are not sufficient to establish that this patient's phenotype is highly specific for a single-gene disease, so PP4 cannot be assessed.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• No patient phenotype or family-history description was available in the reviewed case evidence.

Still missing

• Patient-level phenotype and family-history information is required.

Reasoning

BS2 is not assessed. The population evidence documents absence from gnomAD v2.1 and v4.1, but it does not identify any healthy adult individual carrying this variant in the heterozygous, homozygous, or hemizygous state. The case also supplies no phenotype-confirmed healthy-adult observation and no disease-specific penetrance assessment sufficient to establish the full-penetrance early-onset condition required by BS2.

Rule

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.

Evidence considered

• gnomAD v2.1 and v4.1 report the variant as absent; absence does not provide the healthy-adult carrier observation required for BS2.
• No case source in the supplied evidence documents a healthy adult with this exact variant or a homozygous/hemizygous observation.

Still missing

• A documented healthy adult carrying NM_023110.3:c.1638C>A is needed to evaluate BS2.
• The applicable disorder's inheritance, age-related penetrance, and whether full penetrance is expected at an early age are not established for this criterion.

Sources

Reasoning

No reviewed source provides a well-established variant-specific in vitro or in vivo study showing no damaging effect on FGFR1 protein function or splicing. The available reports describe tumor-associated activating alterations rather than a validated benign functional result, so BS3 cannot be assessed.

Rule

BS3: Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Still missing

• A variant-specific assay showing no damaging effect on protein function or splicing is needed.
• Assay controls, biological relevance, validation, reproducibility, and robustness are not documented.

Reasoning

No affected family members with known variant status are described, so lack of segregation cannot be evaluated. The available tumor studies do not provide a family pedigree or non-segregation observations, and there is no information to assess phenocopies or the possibility of more than one pathogenic variant in an autosomal dominant family.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• PMID:31250151 reports tumor samples without family-level variant testing or non-segregation data.
• PMID:26810070 reports tumor findings without affected-relative testing or a pedigree.
• No affected-family-member non-segregation evidence is present in the available records.

Still missing

• Affected family members and their variant results must be documented.
• A family pedigree and phenotype assessment are required to distinguish true non-segregation from phenocopies.
• The possibility of more than one pathogenic variant in the family must be considered if applicable.

Sources

Reasoning

The variant is missense, but the supplied evidence does not establish that FGFR1 is a gene for which primarily truncating variants are known to cause disease. The available FGFR1 literature instead documents recurrent activating missense variants in the kinase domain, but it does not provide a comprehensive gene-level comparison demonstrating the BP1 premise or its exclusion.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The variant consequence is missense: p.Asn546Lys.
• PMID:31250151 and PMID:26810070 document recurrent activating FGFR1 missense variants, but the supplied sources do not establish the gene-wide premise required to apply or exclude BP1.

Still missing

• A comprehensive FGFR1 disease-mechanism assessment comparing truncating and missense pathogenic variants is needed.

Sources

Reasoning

BP2 is not assessed. The governing rule requires observation in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observation in cis with a pathogenic variant in any inheritance pattern. PMID:26810070 reports the case variant's corresponding FGFR1 N544K together with R659L on different alleles in tumor LGNT34, supporting trans phase, but the available evidence does not establish R659L as pathogenic and does not establish that the observation concerns a fully penetrant dominant FGFR1 disorder. No cis pathogenic-variant observation is reported.

Rule

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

• Genetic alterations in uncommon low-grade neuroepithelial tumors, Results: in tumor LGNT34, two FGFR1 mutations, N544K and R659L, were identified on different alleles; N544K corresponds to the case variant p.(N546K) under the transcript numbering used here.
• The source documents different alleles but does not provide sufficient evidence to classify R659L as pathogenic or to establish a fully penetrant dominant FGFR1 disorder.

Still missing

• The partner R659L variant must be independently established as pathogenic.
• A fully penetrant dominant FGFR1 disorder must be established for the trans pathway, or a pathogenic cis variant must be documented.

Sources

Reasoning

No case-level evidence establishes that this variant was found in a patient with an alternate molecular basis for disease. Reports of the variant in tumors and multiple ClinVar condition labels do not by themselves demonstrate an alternate molecular diagnosis in the relevant case, so BP5 is not assessed.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• The available records do not document a patient-level alternate pathogenic variant, copy-number change, chromosomal abnormality, or other molecular diagnosis coexisting with this exact variant in the relevant disease case.

Still missing

• A documented case with this variant and an independently established alternate molecular basis for the disease is required.