NTRK1 c.655G>A, p.(Gly219Arg)

Reasoning

PM2 is met at supporting strength. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and is present only once in gnomAD v4.1 (total AF=6.44121e-07; 1/1,552,504 alleles; 0 homozygotes). This is an extremely rare population frequency consistent with PM2 supporting under the generic ACMG/AMP framework, although the single observed allele means the variant is not strictly absent from all population databases.

Rule

Generic ACMG/AMP PM2: supporting evidence for absence or an extremely low allele frequency in population databases, interpreted with disease prevalence, penetrance, and inheritance; no applicable NTRK1 VCEP specification was retrieved.

Evidence considered

• gnomAD v2.1 reports AC=0, AN=156,394, AF=0, and 0 homozygotes.
• gnomAD v4.1 reports AC=1, AN=1,552,504, AF=6.44121e-07, and 0 homozygotes; the highest ancestry-specific AF is 8.71347e-07 in non-Finnish Europeans.
• gnomAD-Canada v1.0 reports the variant as absent.
• Generic ACMG/AMP PM2 supporting evidence was applied for absence or extremely low frequency in population databases; the observed single allele is treated as extremely rare rather than absent.

Still missing

• No NTRK1-specific population-frequency or disease-prevalence specification was retrieved.
• The case bundle does not provide a quantitative penetrance/prevalence-based maximum credible allele frequency for NTRK1-related disease.

Sources

Reasoning

REVEL score = 0.217 falls at or below the ClinGen SVI-calibrated REVEL benign-supporting threshold of <=0.290 (Pejaver et al., PMID 36413997), meeting BP4 at the supporting strength via the missense in-silico pathway. It does not reach the moderate benign threshold (<=0.183). SpliceAI max delta = 0.168 is low and not consistent with splice disruption, qualitatively concordant with a benign computational signal but not independently used to strengthen BP4 given the absence of a named calibration publication for this SpliceAI threshold. BayesDel score is present but excluded per pipeline policy (no verified published threshold with a citable PMID/table). No VCEP-specific gene lookup spreadsheet pre-assigns a code for NTRK1. Applying BP4 supporting based on REVEL only, per generic ACMG/AMP with published SVI calibration; not double-counted against PP3 or BP7 (variant is missense, BP7 not applicable).

Rule

Generic ACMG/AMP 2015 (no VCEP-specific PP3/BP4 spreadsheet available for NTRK1); REVEL threshold per ClinGen SVI calibration (PMID 36413997)

Evidence considered

• REVEL score = 0.217 for NM_002529.3:c.655G>A (source_registry key 'revel'); ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID 36413997) sets the benign-supporting threshold at REVEL <=0.290 — 0.217 meets this threshold, supporting BP4 at supporting strength.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.168; source_registry key 'spliceai'); this is qualitatively concordant with the benign computational prediction but is not used to elevate BP4 strength because no named calibration publication for this specific SpliceAI threshold was applied in this evaluation.
• No ClinGen VCEP cspec or gene-specific PP3/BP4 lookup spreadsheet was located for NTRK1 (cspec.found=false; final_classification_framework source='generic_acmg_fallback'), so no pre-assigned code applies.

Still missing

• No gene-specific VCEP framework or PP3/BP4 lookup spreadsheet available for NTRK1
• BayesDel score present but excluded from evidentiary use due to lack of a verified published calibration threshold with a citable PMID
• SpliceAI low score is qualitatively concordant but not used quantitatively for BP4 due to lack of a named calibration publication for the splice-specific threshold

Sources

Reasoning

NM_002529.3:c.655G>A (p.Gly219Arg) in NTRK1 is a missense substitution. No ClinGen VCEP-specific cspec or PP3/BP4 lookup spreadsheet was found for NTRK1 (cspec.found=false; vcep_materials source=generic_acmg_fallback), so generic ACMG in-silico evidence applies. REVEL score = 0.217, well below the ClinGen SVI-calibrated REVEL supporting-pathogenic threshold of >=0.644 (Pejaver et al., PMID 36413997), so REVEL does not support PP3. SpliceAI max delta score = 0.168 (DS_AG), below the commonly used significant-impact threshold of 0.2 and not corroborated by a named calibration publication in this evaluation, so it likewise does not support a splice-damaging call. BayesDel score (-0.171876) is available but per pipeline policy is treated as insufficiently calibrated (no verified published PP3/BP4 threshold with a named PMID/table available to this evaluation) and is not used to call PP3/BP4. No aGVGD data available. No gene-specific PP3 lookup spreadsheet pre-assigns a code. Overall in-silico evidence does not meet PP3.

Rule

Generic ACMG/AMP 2015 (no VCEP-specific PP3/BP4 spreadsheet available for NTRK1); REVEL threshold per ClinGen SVI calibration (PMID 36413997)

Evidence considered

• REVEL score = 0.217 for NM_002529.3:c.655G>A (source_registry key 'revel'); ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID 36413997) sets the pathogenic-supporting threshold at REVEL >=0.644 — 0.217 is far below this, so PP3 is not supported by REVEL.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.168, DS_AG=0.168, DS_AL=0.0, DS_DG=0.126, DS_DL=0.0; source_registry key 'spliceai'); this low delta does not support a splice-damaging (PP3) call.
• No ClinGen VCEP cspec or gene-specific PP3/BP4 lookup spreadsheet was located for NTRK1 (cspec.found=false; final_classification_framework source='generic_acmg_fallback'), so no pre-assigned code applies.

Still missing

• No gene-specific VCEP framework or PP3/BP4 lookup spreadsheet available for NTRK1
• BayesDel score present but excluded from evidentiary use due to lack of a verified published calibration threshold with a citable PMID
• aGVGD score not available in the evidence bundle

Sources

Reasoning

BA1 is not met. The variant has a total allele frequency of 6.44121e-07 in gnomAD v4.1 (1/1,552,504 alleles), with the highest reported ancestry-specific frequency of 8.71347e-07 in the non-Finnish European group; gnomAD v2.1 reports 0/156,394 alleles. These frequencies are far below the generic stand-alone benign threshold of greater than 5%.

Rule

Generic ACMG/AMP BA1: stand-alone benign when population frequency is greater than 5%; no applicable NTRK1 VCEP specification was retrieved.

Evidence considered

• gnomAD v4.1 reports total AC=1, AN=1,552,504, AF=6.44121e-07, with 0 homozygotes; the maximum reported population AF is 8.71347e-07 in non-Finnish Europeans.
• gnomAD v2.1 reports AC=0, AN=156,394, AF=0, with 0 homozygotes.
• Generic ACMG/AMP BA1 stand-alone benign threshold used: allele frequency greater than 5%.

Sources

Reasoning

BS1 is not met. The observed frequency is not greater than expected for a disease-causing variant: gnomAD v4.1 shows AF=6.44121e-07 overall and 8.71347e-07 in the highest-frequency ancestry group, while gnomAD v2.1 shows AF=0. These values are far below the generic BS1 population-frequency range used for variants occurring too frequently for the associated disease.

Rule

Generic ACMG/AMP BS1: supporting benign evidence when the allele frequency is greater than expected for the disorder; assess against disease prevalence, penetrance, and inheritance when available.

Evidence considered

• gnomAD v4.1 reports one allele among 1,552,504 total alleles (AF=6.44121e-07) and one allele among 1,147,648 non-Finnish-European alleles (AF=8.71347e-07), with no homozygotes.
• gnomAD v2.1 reports no observed alleles among 156,394 alleles (AF=0), with no homozygotes.
• No disease-prevalence or penetrance model establishes a benign upper-frequency threshold lower than these observed frequencies; the available frequencies do not support BS1.

Sources

Reasoning

BS2 is not met. No homozygotes were observed in gnomAD v2.1 (0) or gnomAD v4.1 (0). The population data therefore provide no observation of an unaffected healthy adult homozygous for this variant; absence of homozygotes cannot be converted into BS2 evidence.

Rule

Generic ACMG/AMP BS2: supporting benign evidence requires observation of the variant in healthy adults in a genotype that would be expected to cause disease (for a recessive disorder, homozygous); no such observation is available.

Evidence considered

• gnomAD v2.1 reports homozygote count=0 for the variant.
• gnomAD v4.1 reports homozygote count=0 overall and homozygote count=0 in every reported ancestry group.
• No affected/unaffected individual-level segregation or clinically characterized healthy homozygote observation is present in the case evidence bundle.

Sources

Reasoning

PS1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No proband-level de novo evidence is documented in the consolidated case-evidence bundle. There is no parental testing result, maternity/paternity confirmation, or statement that the variant is absent in both tested parents; therefore PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with maternity and paternity confirmed; strength depends on the quality of de novo evidence.

Evidence considered

• The case bundle identifies the variant as NM_002529.3:c.655G>A in NTRK1 but contains no family structure, proband-level clinical record, parental genotype results, or de novo assessment.
• No applicable NTRK1 ClinGen/VCEP specification was retrieved; generic ACMG/AMP criteria were therefore the fallback framework.

Still missing

• Proband phenotype and case identifier
• Genotype results for both biological parents
• Confirmation of maternity and paternity
• Testing method, coverage, and sensitivity for parental samples

Reasoning

No functional/validated-assay evidence for NM_002529.3:c.655G>A (NP_002520.2:p.Gly219Arg) is available in this case's evidence bundle. No CSPEC/VCEP framework exists for NTRK1 (framework_mode: generic_acmg, cspec.found: false). literature_pass.json returned zero PMIDs for this case, and fulltext_map.json is empty, so no published functional/biochemical study (e.g. kinase activity assay, transformation assay, in vitro phosphorylation) mentioning this specific variant was located. OncoKB was queried and explicitly returned no variant-specific reviewed functional evidence (classification: Unknown Oncogenic Effect, is_variant_specific: false), only gene-level context that NTRK1 fusions are oncogenic in various cancers, which is not variant-specific and cannot support PS3.

Evidence considered

• review_manifest.json/case_summary.json show cspec.found=false and framework_mode=generic_acmg, so no NTRK1-specific VCEP functional assay calibration is available
• literature_pass.json total_pmids=0 with note 'No PMIDs found across evidence sources', and fulltext_map.json is empty, indicating no functional publication was retrieved for this variant
• evidence.json oncokb result: evidence_sentence states OncoKB did not identify variant-specific reviewed functional evidence for this variant; is_variant_specific=false, not_reviewed=true, citations_pmids=[]

Still missing

• No validated functional assay (kinase activity, cell transformation/proliferation, phosphorylation) has been located for this specific variant
• No CSPEC/VCEP-specific PS3 assay validation criteria available for NTRK1 to calibrate strength if evidence is later found
• Literature search returned zero PMIDs; a targeted search for NTRK1 p.G219R functional characterization was not possible within the retrieved sources

Reasoning

PS4 requires a statistically significant excess of the variant in affected individuals relative to an appropriate control population, or an equivalent validated case-control enrichment analysis. The case-evidence bundle contains no affected-case counts, control counts, odds ratio, statistical test, or variant-specific case series for NM_002529.3:c.655G>A (NTRK1 p.Gly219Arg).

Rule

Generic ACMG/AMP PS4: prevalence of the variant in affected individuals is significantly increased compared with controls; apply only with appropriate case-control or equivalent validated enrichment evidence.

Evidence considered

• The consolidated case-evidence bundle reports no literature PMIDs and no variant-specific case-control evidence for NM_002529.3:c.655G>A.
• No PS4 evidence can be established from the available records without variant-specific affected and control data.

Still missing

• Variant-specific affected-case and control counts are unavailable.
• No case-control enrichment statistic or validated phenotype prevalence analysis is available.

Reasoning

PM1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No case-level observations of the variant in affected probands, no identified pathogenic or likely pathogenic second allele, and no phasing or inheritance data are present in the consolidated evidence bundle. Therefore, the recessive allelic evidence required for PM3 cannot be assessed.

Rule

Generic ACMG/AMP 2015 PM3: pathogenic variants in trans with the variant in an affected individual support a recessive disease mechanism; strength depends on the number and quality of independent observations and phase evidence.

Evidence considered

• The case summary identifies NTRK1 NM_002529.3:c.655G>A (NP_002520.2:p.(Gly219Arg)) but contains no affected-proband, second-allele, phase, or inheritance observations.
• The consolidated bundle reports no ClinVar record and no literature PMIDs for this case; no publication was available for selective review.
• The bundle states that no ClinGen CSPEC/VCEP or other gene-specific framework was found, so generic ACMG/AMP 2015 allelic criteria apply.

Still missing

• Affected-proband observations for NM_002529.3:c.655G>A are unavailable.
• No pathogenic or likely pathogenic variant in the same gene is documented in trans.
• No parental testing, segregation, or phase information is available.
• No applicable NTRK1 VCEP or gene-specific framework was found; generic ACMG/AMP 2015 is used as fallback.

Reasoning

PM5 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No suspected de novo occurrence without confirmed maternity and paternity is documented. The bundle provides no proband report, parental testing, or family-history information, so PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence, but without confirmation of maternity and paternity; apply only when the available case evidence supports a suspected de novo event.

Evidence considered

• The consolidated case-evidence bundle contains no segregation/de novo observations, parental genotypes, or family-history data for NM_002529.3:c.655G>A.
• No specific publication was identified or reviewed for this criterion because the literature packet contains zero PMIDs and no variant-specific family report.

Still missing

• Proband phenotype and case identifier
• Evidence that the variant is absent from available parental samples or suspected de novo based on family history
• Maternity and paternity information
• Parental testing methodology and limitations

Reasoning

No affected relatives, unaffected relatives, informative meioses, or variant genotype/phenotype co-segregation data are documented. PP1 therefore cannot be assessed.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members; strength may be increased with additional informative meioses when justified by validated quantitative or gene-specific guidance.

Evidence considered

• The case bundle contains no pedigree, relative testing results, affected/unaffected status, or meiosis count for this NTRK1 variant.
• The literature packet contains no papers with variant-specific segregation observations.

Still missing

• Pedigree and affected-relative information
• Genotypes for relatives
• Phenotype status and diagnostic certainty for each relative
• Number of informative meioses and segregation observations

Reasoning

PP2 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single-gene etiology. The case-evidence bundle provides no patient phenotype, family history, diagnostic indication, or phenotype-to-disease concordance assessment for this variant.

Rule

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

Evidence considered

• The consolidated case-evidence bundle contains no patient-level phenotype or family-history information.
• Gene-level disease context alone is insufficient to apply PP4 without a documented, highly specific patient phenotype.

Still missing

• Patient phenotype and diagnostic indication are unavailable.
• Family history and assessment of phenotype specificity for an NTRK1-associated disorder are unavailable.

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel assertion of Pathogenic or Likely pathogenic. The available ClinVar query found no exact record for NM_002529.3:c.655G>A, and the submission audit is empty; therefore no qualifying expert-panel assertion is available.

Rule

Case-specific PP5 rule: apply supporting PP5 only when the exact variant has a ClinVar expert-panel classification of Pathogenic or Likely pathogenic; do not use ordinary laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• ClinVar returned no exact result for NM_002529.3:c.655G>A; no variation ID, classification, review status, or expert-panel submission was available.
• Ordinary submissions, aggregate labels, and non-expert assertions were not used and cannot trigger PP5.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is present.

Sources

Reasoning

No functional assay evidence of any kind (supporting benign or pathogenic effect) is available for this variant in the case bundle. As with PS3, no CSPEC/VCEP framework exists for NTRK1, literature_pass.json found zero PMIDs, fulltext_map.json is empty, and OncoKB returned only non-variant-specific gene-level context with no reviewed functional data. There is no validated assay showing normal/wild-type function for p.Gly219Arg to support BS3.

Evidence considered

• review_manifest.json/case_summary.json show cspec.found=false and framework_mode=generic_acmg, so no NTRK1-specific VCEP functional assay calibration is available
• literature_pass.json total_pmids=0 with note 'No PMIDs found across evidence sources', and fulltext_map.json is empty, indicating no functional publication was retrieved for this variant
• evidence.json oncokb result: evidence_sentence states OncoKB did not identify variant-specific reviewed functional evidence for this variant; is_variant_specific=false, not_reviewed=true, citations_pmids=[]

Still missing

• No functional assay data (of any direction) located for this specific variant
• No CSPEC/VCEP-specific BS3 assay validation criteria available for NTRK1
• Literature search returned zero PMIDs for this variant

Reasoning

No affected relatives who were tested for the variant, and no reliable non-segregation observations, are documented. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; apply only when affected relatives are informative, have reliable phenotype assessments, and do not carry the variant, accounting for phenocopies and reduced penetrance.

Evidence considered

• The consolidated case-evidence bundle contains no family members, parental or relative genotype results, phenotype assessments, or non-segregation data.
• No publication was reviewed for BS4 because no variant-specific family evidence was available in the case literature packet.

Still missing

• Pedigree and phenotype ascertainment
• Genotype results in affected relatives
• Diagnostic confirmation and phenotype consistency for each affected relative
• Number of informative non-segregating meioses and assessment of phenocopies or reduced penetrance

Reasoning

BP1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No case-level phase data show NM_002529.3:c.655G>A in cis with a pathogenic variant or in trans with a benign variant. No family or affected/unaffected proband genotype observations are available, so BP2 cannot be assessed.

Rule

Generic ACMG/AMP 2015 BP2: the variant is observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or in cis with a pathogenic variant for a recessive disorder; application requires documented phase and appropriate inheritance context.

Evidence considered

• The consolidated case-evidence bundle contains no family genotypes, phase information, or comparator benign/pathogenic alleles relevant to BP2.
• The bundle reports no ClinVar record and no literature PMIDs for this case; no publication was available for selective review.
• The bundle states that no ClinGen CSPEC/VCEP or other gene-specific framework was found, so generic ACMG/AMP 2015 allelic criteria apply.

Still missing

• No phased genotype data are available.
• No pathogenic variant in cis or benign variant in trans is documented.
• No parental testing, segregation, or inheritance information is available.
• No applicable NTRK1 VCEP or gene-specific framework was found; generic ACMG/AMP 2015 is used as fallback.

Reasoning

BP5 requires the variant to be found in a case with an alternative molecular basis for the patient's disease. No patient-level case, phenotype, alternative pathogenic molecular finding, or segregation context is provided for this variant.

Rule

Generic ACMG/AMP BP5: variant found in a case with an alternative molecular basis for the disease.

Evidence considered

• The consolidated case-evidence bundle contains no patient case details or alternative molecular diagnosis for NM_002529.3:c.655G>A.
• Absence of a qualifying case prevents assessment of BP5; population frequency data do not establish BP5.

Still missing

• No affected case with an independently established alternative molecular diagnosis is available.
• No patient phenotype or molecular differential-diagnosis data are available.

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel assertion of Benign or Likely benign. The available ClinVar query found no exact record for NM_002529.3:c.655G>A, and the submission audit is empty; therefore no qualifying expert-panel assertion is available.

Rule

Case-specific BP6 rule: apply supporting BP6 only when the exact variant has a ClinVar expert-panel classification of Benign or Likely benign; do not use ordinary laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• ClinVar returned no exact result for NM_002529.3:c.655G>A; no variation ID, classification, review status, or expert-panel submission was available.
• Ordinary submissions, aggregate labels, and non-expert assertions were not used and cannot trigger BP6.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign classification is present.

Sources