ETV6 c.642G>A, p.(Pro214=)

Reasoning

Met. The African/African American gnomAD v4.1 allele frequency is 2.13033% (1598/75012 alleles; 21 homozygotes), with a grpmax filtering allele frequency of 2.04335%; this exceeds the generic non-VCEP BA1 threshold of 1%.

Rule

Generic non-VCEP BA1: maximum credible population allele frequency >1%.

Evidence considered

• No ETV6 ClinGen VCEP specification was retrieved; generic ACMG/AMP population-frequency operating thresholds apply.
• gnomAD v4.1: African/African American AF 0.0213033 (1598/75012), 21 homozygotes, and grpmax FAF 0.0204335.
• The independent gnomAD v2.1 dataset is concordant: African/African American AF 0.0216363 (540/24958), 10 homozygotes, and grpmax FAF 0.0207937.

Sources

Reasoning

NM_001987.4:c.642G>A is a synonymous variant (NP_001978.1:p.(Pro214=)) with no predicted impact on splicing per SpliceAI (max delta score = 0.003, far below any threshold indicating splice disruption, across acceptor/donor gain/loss). This satisfies the SpliceAI component of BP7 for a silent variant with no predicted splicing consequence. No nucleotide-level conservation score (e.g. GERP/phyloP) was present in the case evidence bundle to independently confirm low conservation, which is noted as a residual gap, but the strongly negative SpliceAI prediction and the intronic-distance-appropriate design of the SpliceAI lookup (basic model, 500bp window) support applying BP7 at supporting strength.

Evidence considered

• SpliceAI Lookup (source_registry key 'spliceai') for NM_001987.4:c.642G>A: max delta score = 0.003, described as 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00)' (evidence_brief.json spliceai.sentence); no acceptor/donor gain or loss scores were flagged as significant.
• Variant is synonymous at the protein level: NP_001978.1:p.(Pro214=) / p.(P214=) per case_summary.json normalization, confirming BP7 (silent variant) applicability rather than a missense change.

Still missing

• No explicit nucleotide conservation score (GERP/phyloP) was present in the evidence bundle to independently corroborate low conservation at this position, which is part of the classic two-part BP7 test alongside the splice prediction.

Sources

Reasoning

Not met. The variant is common in population data, particularly in the African/African American population (gnomAD v4.1 AF 2.13033%; grpmax FAF 2.04335%), and is not absent or rare enough for PM2.

Rule

Generic non-VCEP PM2 requires absence or an extremely low population frequency; the observed maximum population frequency is incompatible with PM2.

Evidence considered

• gnomAD v4.1: total AF 0.11889% (1919/1614094), African/African American AF 2.13033% (1598/75012), 22 total homozygotes, and grpmax FAF 2.04335%.
• gnomAD v2.1 independently reports African/African American AF 2.16363% (540/24958), 10 homozygotes, and grpmax FAF 2.07937%.
• gnomAD-Canada v1.0 also reports the variant (32/18416 alleles; AF 0.17376%).

Sources

Reasoning

No case-level proband phenotype, parental genotypes, parentage confirmation, or de novo testing result is provided. Therefore, confirmed de novo evidence cannot be assessed.

Rule

Generic ACMG/AMP PS2: apply only when the variant is demonstrated de novo in an affected individual with maternity and paternity confirmed.

Evidence considered

• No ETV6 CSPEC, VCEP material, or local gene-specific framework was retrieved; generic ACMG/AMP evaluation is therefore applicable.
• The consolidated case-evidence bundle contains no case-level parental testing, parentage, proband phenotype, or de novo observation for NM_001987.4:c.642G>A.

Still missing

• Obtain a molecular result for the proband and both biological parents for NM_001987.4:c.642G>A.
• Document biological parentage confirmation and whether the proband phenotype is consistent with an ETV6-associated disorder.

Reasoning

No validated functional assay data (e.g., transcriptional repression, DNA-binding, nuclear localization, minigene/RT-PCR splicing assay) specific to NM_001987.4:c.642G>A (p.(P214=)) was found in the case bundle. SpliceAI predicts no significant splice impact (max delta score = 0.00), but this is a computational prediction, not a validated functional assay, and is therefore not eligible evidence for PS3. The splicing-mutation resource paper (PMID:31275557) is a pan-cancer database of validated splicing mutations but does not mention this specific variant or gene position on text search of its full text, so it cannot be grounded to this variant. No other functional study of this variant was identified.

Still missing

• No variant-specific functional assay (transcriptional repression, DNA-binding, nuclear localization, or RNA/splicing assay) available for c.642G>A
• SpliceAI score alone is insufficient for PS3 (requires validated functional/splicing assay, not computational prediction)

Reasoning

No variant-specific case-control or statistically valid enrichment data were retrieved for ETV6 c.642G>A (p.Pro214=).

Rule

Generic ACMG/AMP PS4 requires the variant to be significantly enriched in affected individuals compared with controls.

Evidence considered

• The literature triage contains no ETV6 c.642G>A case-control study. Its sole PS4 candidate, PMID:24121147, is an alpha-1-antitrypsin newborn-screening paper and is not relevant to ETV6 or this variant.

Still missing

• A variant-specific case-control study or other statistically valid enrichment dataset with affected and control counts is required.

Reasoning

No affected-proband observation pairs this variant with a pathogenic/likely pathogenic ETV6 variant in confirmed trans. ETV6 has no applicable VCEP/gene-specific specification in the case materials, so generic ACMG/AMP cis/trans guidance was used.

Rule

Generic ACMG/AMP PM3: moderate evidence requires the assessed variant to be observed in trans with a pathogenic variant in an affected individual with a recessive disorder; no qualifying observation is available.

Evidence considered

• The case bundle reports no ETV6 CSPEC/VCEP framework, no local gene framework, and generic ACMG/AMP fallback.
• The available ClinVar material contains only single-submitter classifications without criterion leads or validated case-level publications; it provides no pathogenic co-variant, phase, or affected-proband observation for this variant.
• PMID:25741868 states that, for a recessive disorder, a heterozygous variant found in trans with a known pathogenic variant can support PM3; no such observation is available here.

Still missing

• Affected-proband data identifying a second ETV6 pathogenic/likely pathogenic variant.
• Parental or other validated phasing evidence demonstrating that NM_001987.4:c.642G>A is in trans with that variant in a disorder with a recessive ETV6 mechanism.

Sources

Reasoning

No case-level parental genotypes or de novo testing result is provided. Unconfirmed de novo evidence cannot be assessed.

Rule

Generic ACMG/AMP PM6: apply only when de novo occurrence in an affected individual is reported but parentage is not confirmed.

Evidence considered

• No ETV6 CSPEC, VCEP material, or local gene-specific framework was retrieved; generic ACMG/AMP evaluation is therefore applicable.
• The consolidated case-evidence bundle contains no case-level parental testing, parentage, proband phenotype, or de novo observation for NM_001987.4:c.642G>A.

Still missing

• Obtain molecular testing results for both biological parents and the proband for NM_001987.4:c.642G>A.
• If the variant is absent from both parents, document whether parentage has been confirmed.

Reasoning

No family pedigree, relative genotypes, affected-status data, or informative meioses are provided. Segregation with an ETV6-associated phenotype cannot be assessed.

Rule

Generic ACMG/AMP PP1: apply only when the variant cosegregates with disease in multiple affected family members; the weight depends on the amount and quality of segregation evidence.

Evidence considered

• No ETV6 CSPEC, VCEP material, or local gene-specific framework was retrieved; generic ACMG/AMP evaluation is therefore applicable.
• The consolidated case-evidence bundle contains no family-specific genotype-phenotype co-segregation data or informative meioses for NM_001987.4:c.642G>A.

Still missing

• Provide a pedigree with relatives' phenotypes and molecular results for NM_001987.4:c.642G>A.
• Provide the number of informative meioses and ascertainment context.

Reasoning

No proband phenotype, diagnostic indication, or phenotype-specific testing context was supplied from which a highly specific ETV6-associated phenotype could be assessed.

Rule

Generic ACMG/AMP PP4 requires a patient phenotype or family history highly specific for a disease with a single genetic etiology.

Evidence considered

• The available ClinVar condition labels are nonspecific or unrelated (inborn genetic diseases, melanoma, not provided, and not specified) and do not establish a phenotype for the proband.

Still missing

• Provide the proband phenotype, age of onset, family history, and relevant differential diagnoses to assess phenotype specificity.

Reasoning

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

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar matches the exact variant, but the audit reports zero expert-panel submissions; the available submissions are ordinary single-submitter Benign or Likely benign assertions and cannot trigger PP5.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is required.

Sources

Reasoning

The population datasets report homozygote counts but do not provide phenotypes, age, or disease-status data for individual carriers. Therefore they cannot establish observation in healthy adults for BS2.

Rule

Generic ACMG/AMP BS2 requires observation in healthy adults for a fully penetrant disorder expected to have early onset.

Evidence considered

• gnomAD v4.1 reports 22 total homozygotes (21 African/African American), and gnomAD v2.1 reports 10 total homozygotes; neither source supplies individual clinical phenotype or age information needed for BS2.

Still missing

• Phenotyped, age-appropriate observations of unaffected homozygous or heterozygous carriers for the relevant ETV6-associated condition are not available in the case evidence.

Sources

Reasoning

No validated functional assay data demonstrating normal/wild-type function for NM_001987.4:c.642G>A was found. This is a synonymous variant (p.(P214=)) with SpliceAI predicting no significant splice impact (max delta score = 0.00), consistent with lack of splicing disruption, but this is a computational prediction and not a validated functional assay eligible for BS3. No RNA-based (RT-PCR/minigene) or protein-functional study of this specific variant was identified in the case materials.

Still missing

• No variant-specific functional assay (e.g., RNA splicing assay, protein function assay) demonstrating normal function is available for c.642G>A
• SpliceAI prediction of no splice impact is supportive computational evidence only, not a substitute for a validated functional assay required for BS3

Reasoning

No informative family data show lack of segregation between NM_001987.4:c.642G>A and a relevant phenotype. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: apply only when the variant demonstrably fails to segregate with disease in informative relatives, after considering penetrance, age of onset, and phenocopies.

Evidence considered

• No ETV6 CSPEC, VCEP material, or local gene-specific framework was retrieved; generic ACMG/AMP evaluation is therefore applicable.
• The consolidated case-evidence bundle contains no family-specific genotype-phenotype discordance or other informative non-segregation evidence for NM_001987.4:c.642G>A.

Still missing

• Provide molecular results and relevant phenotype status for informative affected and unaffected relatives.
• Document pedigree structure, ages, and penetrance-relevant clinical evaluation so any observed non-segregation can be interpreted.

Reasoning

No co-occurrence and phase observation is available. Therefore, there is no evidence that this variant is in cis with a pathogenic ETV6 variant in a recessive setting or in trans with a pathogenic ETV6 variant in a dominant setting.

Rule

Generic ACMG/AMP BP2: supporting benign evidence may be used for a qualifying cis/trans observation with a pathogenic variant, interpreted in the relevant inheritance context; no qualifying co-occurrence is available.

Evidence considered

• The case bundle reports no ETV6 CSPEC/VCEP framework, no local gene framework, and generic ACMG/AMP fallback.
• The available ClinVar material contains only single-submitter classifications without criterion leads or validated case-level publications; it provides no co-occurring pathogenic variant or phase information.
• PMID:25741868 describes BP2 as supporting evidence from a pathogenic-variant co-occurrence with the relevant cis/trans configuration; the required observation is absent.

Still missing

• A documented pathogenic/likely pathogenic ETV6 co-variant in the same individual.
• Validated phasing and disease-context information showing a BP2-qualifying cis or trans configuration.

Sources

Reasoning

No proband-level evidence identifies an alternate molecular diagnosis that fully explains the reported phenotype.

Rule

Generic ACMG/AMP BP5 requires an alternate molecular cause in a patient whose phenotype is explained by that alternate diagnosis.

Evidence considered

• No case-level phenotype or alternate molecular diagnosis is present in the supplied evidence bundle.

Still missing

• Provide phenotype information and the complete diagnostic testing result, including any independently diagnostic variant, to evaluate an alternate cause.

Reasoning

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

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar matches the exact variant, but the audit reports zero expert-panel submissions; the aggregate benign label and ordinary laboratory Benign/Likely benign submissions cannot trigger BP6.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign assertion is required.

Sources