MPL c.1494_1495insGTGATCGCTCTG, p.(Leu498_His499insValIleAlaLeu)

Reasoning

No applicable MPL-specific VCEP or gene framework was identified, so the generic ClinGen SVI PM2 recommendation applies. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, consistent with an allele frequency <=0.0001; PM2 is met at supporting strength.

Rule

Generic ClinGen SVI PM2: absent or sufficiently rare in population databases, with allele frequency <=0.0001; supporting strength.

Evidence considered

• The governing framework record reports no applicable CSPEC/VCEP or gene-specific framework; generic ACMG/AMP rules therefore apply.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada; no population allele count or frequency was reported.
• The generic ClinGen SVI PM2 recommendation uses an allele-frequency threshold of <=0.0001 and assigns PM2 supporting strength (ClinGen SVI 2020, PMID:25741868).

Sources

Reasoning

PM4 is met at moderate strength under the generic ACMG/AMP framework because NM_005373.2:c.1494_1495insGTGATCGCTCTG produces the in-frame protein insertion NP_005364.1:p.(Leu498_His499insValIleAlaLeu), adding four amino acids without a frameshift or premature termination. The affected sequence lies within the annotated coding exon 10 and the inserted residues are in the hydrophobic MPL transmembrane-region sequence, which is not a repetitive low-complexity protein segment. The protein-length change is therefore a non-repeat in-frame insertion, satisfying the PM4 consequence requirement; no NMD or PVS1 assessment is relevant to this in-frame event.

Rule

Generic ACMG/AMP PM4: protein-length change caused by an in-frame insertion outside a repetitive region.

Evidence considered

• The normalized transcript annotation is NM_005373.2:c.1494_1495insGTGATCGCTCTG, producing NP_005364.1:p.(Leu498_His499insValIleAlaLeu).
• The inserted sequence is 12 nucleotides, corresponding to a four-amino-acid in-frame insertion, so the protein length changes without a frameshift or premature stop.
• Variant Validator places the change in coding exon 10, and the predicted protein sequence places p.Leu498_His499 within the hydrophobic transmembrane-region sequence rather than a repetitive low-complexity segment.
• Generic ACMG/AMP PM4 applies to protein-length changes caused by in-frame insertions or deletions outside repetitive regions.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact variant has no ClinVar result, variation ID, or expert-panel assertion, so PP5 is not met.

Rule

Apply PP5 only when the exact variant has a ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar returned no exact-variant result for NM_005373.2:c.1494_1495insGTGATCGCTCTG; consequently, no expert-panel Pathogenic or Likely pathogenic classification can trigger PP5.
• Ordinary submissions, aggregate labels, and non-expert assertions would not qualify under the specified PP5 rule, and none were identified.

Sources

Reasoning

No applicable MPL-specific VCEP or gene framework was identified, so the generic ACMG/AMP population threshold applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1, with no observed allele frequency approaching the BA1 stand-alone threshold of >=0.05; therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: stand-alone benign when allele frequency is >=0.05.

Evidence considered

• The governing framework record reports no applicable CSPEC/VCEP or gene-specific framework; generic ACMG/AMP rules therefore apply.
• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent, so no allele frequency >=0.05 is observed.
• The generic BA1 threshold is allele frequency >=0.05 (ACMG/AMP 2015, PMID:25741868).

Sources

Reasoning

No applicable MPL-specific VCEP or gene framework was identified, so the generic population threshold applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1, with no observed allele frequency >=0.01; therefore BS1 is not met.

Rule

Generic ACMG/AMP BS1: allele frequency greater than expected for the disorder when frequency is >=0.01.

Evidence considered

• The governing framework record reports no applicable CSPEC/VCEP or gene-specific framework; generic ACMG/AMP rules therefore apply.
• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent, so no allele frequency >=0.01 is observed.
• The generic BS1 threshold is allele frequency >=0.01 (generic SVI default; Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

No applicable MPL-specific VCEP or gene framework was identified, so generic BS2 logic applies. The variant is absent from the available gnomAD population datasets; consequently, there is no observation of the variant in healthy adults or evidence of healthy adult homozygotes, and the BS2 criterion is not met.

Rule

Generic ACMG/AMP BS2: observed in healthy adults, including in healthy adult homozygotes for a dominant disorder or healthy adult homozygotes for a recessive disorder.

Evidence considered

• The governing framework record reports no applicable CSPEC/VCEP or gene-specific framework; generic ACMG/AMP rules therefore apply.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, so no healthy-adult carrier or homozygote observation is available to support BS2.

Sources

Reasoning

BP3 is not met. Although the variant is an in-frame insertion, the available transcript and protein consequence place it at p.Leu498_His499 within the hydrophobic MPL transmembrane-region sequence, not in a repetitive protein region. This region is structurally specific and functionally relevant rather than an in-frame repeat-region insertion with no known function, so the BP3 benign criterion is not applicable to this event.

Rule

Generic ACMG/AMP BP3: in-frame insertion or deletion in a repetitive region without a known function; the required repeat-region context is absent.

Evidence considered

• The variant produces the in-frame insertion NP_005364.1:p.(Leu498_His499insValIleAlaLeu).
• The affected sequence is in the hydrophobic MPL transmembrane-region sequence and does not show a repetitive low-complexity protein context in the provided reference sequence.
• BP3 requires an in-frame insertion or deletion in a repetitive region without a known function; the transmembrane-region context does not satisfy that requirement.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact variant has no ClinVar result, variation ID, or expert-panel assertion, so BP6 is not met.

Rule

Apply BP6 only when the exact variant has a ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar returned no exact-variant result for NM_005373.2:c.1494_1495insGTGATCGCTCTG; consequently, no expert-panel Benign or Likely benign classification can trigger BP6.
• Ordinary submissions, aggregate labels, and non-expert assertions would not qualify under the specified BP6 rule, and none were identified.

Sources

Reasoning

No case-specific clinical pedigree, proband-parent genotypes, parental testing results, maternity or paternity confirmation, or documented de novo observation is available. Therefore, the evidence required to assess PS2 cannot be evaluated.

Rule

Generic ACMG/AMP PS2 requires a confirmed de novo variant in an affected individual with confirmed parentage; strength may be modified by phenotype specificity and parental testing completeness.

Evidence considered

• The available case evidence contains no proband-parent genotype comparison or confirmed de novo finding for NM_005373.2:c.1494_1495insGTGATCGCTCTG.

Still missing

• Proband and both parental variant testing results are not documented.
• Maternity and paternity confirmation are not documented.
• Phenotypic information and confirmation that the proband is affected are not documented.

Reasoning

No validated functional assay evaluating the effect of NM_005373.2:c.1494_1495insGTGATCGCTCTG on MPL function was identified. The available evidence contains no experimental assay, assay controls, quantitative functional result, or biologically relevant rescue or loss-of-function measurement that could support PS3 at any strength. OncoKB likewise reports no variant-specific reviewed functional evidence. Therefore PS3 cannot be assessed rather than inferred from the variant's predicted in-frame protein insertion, somatic database observation, or splice prediction.

Evidence considered

• No paper or case source provided validated assay data for NM_005373.2:c.1494_1495insGTGATCGCTCTG.
• OncoKB reported no variant-specific reviewed functional evidence for this variant.
• The variant is an in-frame insertion, but predicted consequence alone is not functional evidence for PS3.

Still missing

• A validated, biologically relevant MPL functional assay with appropriate positive and negative controls is needed.
• Quantitative assay results and prespecified calibration for PS3 strength are unavailable.

Sources

Reasoning

No applicable MPL-specific VCEP framework was identified, and the case evidence contains no affected-case series, control comparison, odds ratio, likelihood ratio, or other case-control enrichment measure for NM_005373.2:c.1494_1495insGTGATCGCTCTG. Therefore PS4 cannot be assessed from the available evidence.

Rule

PS4 requires a statistically significant excess of the variant in affected individuals compared with controls; no numeric comparison is available here.

Evidence considered

• The case evidence provides no exact-variant case-control counts or enrichment statistic.
• No MPL-specific VCEP or other governing gene-specific framework was available; generic ACMG/AMP rules were therefore the applicable fallback.

Still missing

• A case-control dataset or adequately documented affected-case enrichment analysis for the exact variant is required.

Sources

Reasoning

Generic ACMG/AMP PM3 requires the variant to be observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive disorder, with strength determined by the quality and number of such observations. No affected-proband observation, second pathogenic allele, phase result, or inheritance information is documented for NM_005373.2:c.1494_1495insGTGATCGCTCTG; therefore PM3 cannot be assessed without inventing allelic evidence.

Rule

Generic ACMG/AMP PM3: pathogenic or likely pathogenic variant observed in trans with the evaluated variant in an affected individual with a recessive disorder; strength depends on the number and quality of informative observations.

Evidence considered

• No affected-proband observations, pathogenic or likely pathogenic second allele, phase result, or inheritance information are documented in the available case evidence.

Still missing

• Affected-proband observations are unavailable.
• A pathogenic or likely pathogenic second allele and its phase are unavailable.
• Inheritance information and disease-mode confirmation are unavailable.

Reasoning

No case-specific report of an apparently de novo variant, unconfirmed parental status, proband phenotype, or family testing is available. The evidence is therefore insufficient to assess PM6.

Rule

Generic ACMG/AMP PM6 applies to an apparently de novo variant when parental testing or parentage confirmation is incomplete; evidence must still establish an affected proband and a credible de novo claim.

Evidence considered

• The available case evidence contains no clinical report or family data describing an apparently de novo occurrence of this variant.

Still missing

• An apparently de novo occurrence in the proband is not documented.
• Parental testing or the reason parentage could not be confirmed is not documented.
• Phenotype consistency and clinical ascertainment details are not documented.

Reasoning

No affected or unaffected relatives, informative meioses, segregation counts, variant genotypes, or phenotype assessments are provided. Consequently, co-segregation evidence cannot be assessed at supporting or increased strength.

Rule

Generic ACMG/AMP PP1 requires co-segregation of the variant with disease in affected family members; strength depends on the number and informativeness of meioses and the phenotype specificity.

Evidence considered

• The available case evidence contains no family segregation data for NM_005373.2:c.1494_1495insGTGATCGCTCTG.

Still missing

• Family structure and the number of informative meioses are not documented.
• Relative genotypes and phenotype status are not documented.
• No segregation analysis or quantitative family-level evidence is available.

Reasoning

No individual phenotype, clinical presentation, or disease-specific feature set is provided for this case. Although MPL is associated with myeloproliferative neoplasms in general, gene-level disease context does not establish a highly specific phenotype for this variant under PP4.

Rule

PP4 requires a patient's phenotype or highly specific disease features to be highly specific for the disease associated with the gene; general gene-level association is insufficient.

Evidence considered

• No patient phenotype or clinical feature set is present in the available case evidence.
• OncoKB supplies only general MPL disease context and explicitly does not provide variant-specific reviewed evidence; this is insufficient for PP4.

Still missing

• The patient's confirmed phenotype and its specificity for an MPL-related disorder are required.

Sources

Reasoning

No validated functional assay demonstrating preserved MPL function for NM_005373.2:c.1494_1495insGTGATCGCTCTG was identified. The available evidence contains no experimental assay, assay controls, quantitative functional result, or biologically relevant normal-function measurement that could support BS3 at any strength. The absence of variant-specific reviewed functional evidence in OncoKB does not establish a benign functional effect. Therefore BS3 cannot be assessed.

Evidence considered

• No paper or case source provided validated assay data showing preserved MPL function for NM_005373.2:c.1494_1495insGTGATCGCTCTG.
• OncoKB reported no variant-specific reviewed functional evidence for this variant.
• The absence of functional evidence cannot be treated as evidence of a benign effect for BS3.

Still missing

• A validated, biologically relevant MPL functional assay with appropriate controls is needed to evaluate normal function.
• Quantitative assay results and prespecified calibration for BS3 strength are unavailable.

Sources

Reasoning

No unaffected relatives known to be at risk, reliable familial genotypes, phenotype assessments, or informative non-segregation observations are available. Therefore, BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4 requires a variant not to segregate with disease in affected family members or to be absent in affected relatives when informative family data support non-segregation; phenotype and testing reliability must be adequate.

Evidence considered

• The available case evidence contains no documented unaffected tested relatives who carry or lack the variant in a way that would inform non-segregation.

Still missing

• At-risk unaffected relatives and their clinical status are not documented.
• Relative genotypes and testing quality are not documented.
• No informative non-segregation event is reported.

Reasoning

Generic ACMG/AMP BP2 requires observation of the evaluated variant in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for any disorder, with an appropriate disease and phase context. No second variant, phase result, affected-proband observation, or inheritance information is documented for NM_005373.2:c.1494_1495insGTGATCGCTCTG; therefore BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2: the evaluated variant is observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for any disorder, provided the phase and disease context are informative.

Evidence considered

• No partner pathogenic variant, cis/trans phase result, affected-proband observation, or inheritance information is documented in the available case evidence.

Still missing

• A partner pathogenic variant is unavailable.
• Cis/trans phase information is unavailable.
• Disease inheritance mode and informative affected-proband context are unavailable.

Reasoning

No patient-level disease diagnosis, alternate molecular explanation, or documentation that the phenotype is fully explained by another pathogenic variant is available. The case therefore lacks the clinical evidence required to assess BP5.

Rule

BP5 requires the variant to be found in a patient with a well-established alternative molecular cause for the phenotype; no such patient-level evidence is available.

Evidence considered

• The available case evidence contains no affected individual clinical record, alternate pathogenic variant, or molecular diagnosis that could support BP5.
• No numeric BP5 threshold is applicable because the generic rule is clinical and does not define a likelihood-ratio comparison here.

Still missing

• Patient-level phenotype and a documented alternative molecular cause explaining that phenotype are required.

Sources