DICER1 c.4206+11_4206+13del, p.?

Reasoning

BS1 is met at Strong strength. The ClinGen DICER1 VCEP specification requires frequency >0.0003 in a gnomAD subpopulation with >2,000 alleles tested and at least 5 variant alleles. gnomAD v4.1 shows 0.0026107867 in the East Asian subpopulation (76/29,110 alleles), which exceeds the threshold and satisfies both sample-size conditions. Other qualifying v4 subpopulations also exceed 0.0003, including NFE (456/1,060,752; 0.0004298837), AMR (34/48,548; 0.0007003378), and SAS (20/74,708; 0.0002677 does not exceed the threshold).

Rule

ClinGen DICER1 VCEP v1.4: Frequency >0.0003 (0.03%) in a gnomAD subpopulation; subpopulations must have >2,000 alleles tested and a minimum of 5 alleles present.

Evidence considered

• The DICER1 VCEP v1.4 BS1 rule requires frequency >0.0003 (0.03%) in a gnomAD subpopulation, with >2,000 alleles tested and at least 5 alleles present.
• gnomAD v4.1 reports East Asian frequency 0.0026107867 from 76/29,110 alleles, clearly exceeding the BS1 threshold with adequate allele count and tested-allele count.
• The gnomAD v4.1 result is the most recent and comprehensive population dataset provided, as directed by the VCEP specification.

Sources

Reasoning

BS2 is met at Supporting strength under the DICER1 VCEP rule for 2 or more observations of homozygosity in individuals lacking clinical information. gnomAD v4.1 reports 2 homozygotes overall, with one in the AMR population and one in NFE; gnomAD v2.1 independently reports 6 homozygotes overall. The population records do not provide individual age, tumor history, or parental confirmation, so the stronger BS2 level requiring healthy individuals or parental confirmation is not used. The VCEP's Supporting rule explicitly accommodates homozygous observations in individuals lacking clinical information.

Rule

ClinGen DICER1 VCEP v1.4 BS2 Supporting: 2 or more observations of homozygosity in individuals lacking clinical information. Strong requires 2 or more homozygous observations in healthy individuals, or 1 homozygous healthy individual with parental confirmation.

Evidence considered

• The DICER1 VCEP v1.4 BS2 Supporting rule permits 2 or more observations of homozygosity in individuals lacking clinical information.
• gnomAD v4.1 reports 2 homozygotes for the variant overall; the AMR and NFE subpopulations each report one homozygote.
• gnomAD v2.1 reports 6 homozygotes overall, providing additional population-database observations, but does not provide individual clinical status or parental confirmation.

Still missing

• Individual-level clinical status, age, tumor-free follow-up, and parental phase/confirmation are not available for the gnomAD homozygotes.

Sources

Reasoning

PVS1 is not met. NM_177438.3:c.4206+11_4206+13del is a deep intronic deletion (positions +11 to +13), not a nonsense, frameshift, or canonical splice-site (+/-1 or 2) variant. The DICER1 VCEP PVS1 specification applies its splice-site rules to canonical positions; no RNA evidence demonstrates aberrant splicing, and SpliceAI predicts no significant splice impact (maximum delta 0.012). Thus, there is no established null consequence, NMD prediction, or exon loss on which to apply the DICER1 PVS1 decision tree.

Rule

DICER1 VCEP PVS1: canonical splice variants are restricted to intronic +/-1 or 2 positions; apply the DICER1 NMD/exon decision tree only after a null or splice-disrupting consequence is established.

Evidence considered

• The DICER1 VCEP specification states that PVS1 is used for nonsense/frameshift variants according to NMD and for canonical splice variants at intronic +/-1 or 2 positions, with specified exon-dependent exceptions.
• The normalized MANE-select transcript description is NM_177438.3:c.4206+11_4206+13del with predicted protein consequence p.?, placing the deletion 11 to 13 bases into the intron rather than at a canonical splice position.
• SpliceAI reports a maximum delta score of 0.012 and states that no significant splice impact is predicted.

Still missing

• No RNA assay is available to directly assess whether this deep intronic deletion alters splicing.
• No aberrant transcript, affected exon, reading-frame consequence, or NMD consequence has been established.

Sources

Reasoning

PM2 is not met. The DICER1 VCEP Supporting rule requires allele frequency <0.000005 across gnomAD, no more than one allele in any subpopulation, and at least 20x coverage. gnomAD v4.1 reports total AF 0.000439012 (620/1,412,262 alleles), including 76 alleles in East Asian individuals and 456 in NFE; these observations are far above the PM2 threshold and exceed the one-allele-per-subpopulation condition. The gnomAD v2.1 result is likewise incompatible with PM2 (40/238,676 alleles; 6 homozygotes).

Rule

ClinGen DICER1 VCEP v1.4: Allele frequency <0.000005 across gnomAD with no more than one allele in any subpopulation and at least 20x coverage.

Evidence considered

• The DICER1 VCEP v1.4 PM2 Supporting rule requires allele frequency <0.000005 across gnomAD, no more than one allele in any subpopulation, and at least 20x coverage.
• gnomAD v4.1 reports total AF 0.000439012 from 620/1,412,262 alleles, with 76 East Asian alleles and 456 NFE alleles; this fails both the frequency and subpopulation allele-count requirements.
• gnomAD v2.1 reports total AF 0.000167591 from 40/238,676 alleles and 6 homozygotes, also excluding PM2.

Sources

Reasoning

PM4 is not met. This is an intronic 3-bp deletion with predicted protein consequence p.?, not an established in-frame protein indel or stop-loss. The DICER1 VCEP PM4 specification requires an in-frame indel: Moderate only when a deleted/inserted residue lies in RNase IIIb (p.Tyr1682-p.Ser1846), or Supporting outside RNase IIIb and outside the listed repeat regions. No protein length change, affected residue, RNase IIIb involvement, or repeat-region context can be assigned from the available evidence.

Rule

DICER1 VCEP PM4: in-frame indel involving RNase IIIb (p.Tyr1682-p.Ser1846) = Moderate; in-frame indel outside RNase IIIb and outside p.Asp606-p.Asp609, p.Glu1418-p.Glu1420, and p.Glu1422-p.Glu1425 repeat regions = Supporting.

Evidence considered

• The DICER1 VCEP PM4 rule applies to in-frame indels, at Moderate strength for an affected RNase IIIb residue (p.Tyr1682-p.Ser1846) and at Supporting strength only outside both RNase IIIb and the specified repeat regions.
• Variant normalization gives NP_803187.1:p.? rather than an in-frame protein deletion/insertion.
• SpliceAI predicts no significant splice impact (maximum delta 0.012), providing no computational basis for a splice-derived protein length change.

Still missing

• No RNA or protein data establish an in-frame product or protein length change.
• If aberrant splicing is later demonstrated, the resulting transcript and protein consequence would need assessment before PM4 could be reconsidered.

Sources

Reasoning

BA1 is not met. Under the ClinGen DICER1 VCEP specification, BA1 requires frequency >0.003 in a gnomAD subpopulation with >2,000 alleles tested and at least 5 variant alleles. The most recent comprehensive dataset, gnomAD v4.1, has its highest qualifying subpopulation frequency in East Asian individuals at 0.0026107867 (76/29,110 alleles), below 0.003. The apparently higher gnomAD v2.1 EAS_JPN frequency (0.0080645) is based on only 124 tested alleles and one variant allele, so it does not qualify under the VCEP minimum-size requirements.

Rule

ClinGen DICER1 VCEP v1.4: Frequency >0.003 (0.3%) in a gnomAD subpopulation; subpopulations must have >2,000 alleles tested and a minimum of 5 alleles present.

Evidence considered

• The DICER1 VCEP v1.4 BA1 rule requires frequency >0.003 in a gnomAD subpopulation, with >2,000 alleles tested and at least 5 alleles present.
• gnomAD v4.1 reports the highest qualifying subpopulation frequency in East Asian individuals as 0.0026107867, with 76/29,110 alleles; this is below the BA1 threshold.
• gnomAD v2.1 reports EAS_JPN at 0.0080645, but the estimate is from 1/124 alleles and therefore fails the VCEP subpopulation-size and minimum-allele requirements.

Sources

Reasoning

The DICER1 VCEP permits PS1 for a same-amino-acid change, or for a non-canonical intronic variant at the same nucleotide with equal or worse splicing impact, but requires comparison with a variant asserted pathogenic by the ClinGen DICER1 VCEP. This variant is non-canonical intronic (NM_177438.3:c.4206+11_4206+13del; predicted protein consequence p.?), and no qualifying pathogenic comparator at the same nucleotide or amino-acid change is present in the case evidence. SpliceAI predicts no significant splice impact (maximum delta score 0.012), but that result does not establish the required comparator relationship.

Rule

For same AA change, confirm no difference in splicing using RNA data or concordant MaxEntScan and SpliceAI modeling. For non-canonical intronic splicing variants at the same nucleotide, the variant must have equal or worse splicing impact. The compared variant must be asserted pathogenic by the ClinGen DICER1 VCEP; likely pathogenic changes do not apply.

Evidence considered

• The governing ClinGen DICER1 VCEP Version 1.4 PS1 rule requires a same-amino-acid comparison, or for non-canonical intronic variants a same-nucleotide comparison with equal or worse splicing impact; the comparator must be asserted pathogenic by the ClinGen DICER1 VCEP, not merely likely pathogenic.
• VariantValidator describes NM_177438.3:c.4206+11_4206+13del as intronic in exon 22i with predicted protein consequence NP_803187.1:p.?, so an amino-acid change is not established.
• SpliceAI reports DS_AG 0.012, DS_AL 0.001, DS_DG 0.004, and DS_DL 0.001, with maximum delta score 0.012; this is insufficient by itself to fulfill the required same-variant comparator evidence.

Still missing

• A ClinGen DICER1 VCEP-pathogenic comparator at the same nucleotide or same amino-acid change is not available.
• No RNA or paired comparator splicing evidence is available to establish equal or worse impact under the VCEP PS1 rule.

Sources

Reasoning

The DICER1 VCEP permits PS2 using a point-based de novo framework, but the case-evidence bundle contains no proband-level parental testing results, maternity/paternity confirmation, de novo assertion, phenotype information, or de novo point assignment for this variant. PS2 therefore cannot be assessed.

Rule

DICER1 VCEP PS2: Very Strong for >=4 de novo points; Strong for >=2 and <4; Moderate for >=1 and <2; Supporting for >=0.5 and <1.

Evidence considered

• The governing ClinGen DICER1 VCEP specification defines PS2 as >=4 de novo points for Very Strong, >=2 and <4 points for Strong, >=1 and <2 points for Moderate, and >=0.5 and <1 point for Supporting.
• The consolidated case-evidence bundle provides no case-specific pedigree, parental testing, maternity/paternity confirmation, de novo observation, or phenotype data for NM_177438.3:c.4206+11_4206+13del.

Still missing

• Documented proband phenotype consistent with DICER1-related tumor predisposition
• Parental genotypes demonstrating presence of the variant in neither parent
• Confirmation of maternity and paternity or equivalent relationship testing
• Number and quality of de novo observations or de novo points

Sources

Reasoning

No validated functional study for NM_177438.3:c.4206+11_4206+13del was identified. The DICER1 VCEP specifies PS3 for demonstrated splicing impact or reduced DICER1 pre-miRNA cleavage, with strength calibrated by the RNA result or a controlled cleavage assay; the available record contains neither variant-specific RNA assay data nor cleavage-assay results.

Evidence considered

• The ClinGen DICER1 and miRNA-Processing Gene Expert Panel specification, version 1.4, states that PS3 should be used for functional evidence of splicing impact and/or reduced DICER1 pre-miRNA cleavage; it defines strong and moderate RNA-assay outcomes and a supporting controlled cleavage-assay outcome.
• The case bundle contains no variant-specific RNA or biochemical functional assay result. SpliceAI prediction (maximum delta score 0.012) is computational evidence and does not establish PS3 functional evidence.

Still missing

• Variant-specific RNA assay data are needed to establish whether splicing is altered and, if so, whether the consequence is out-of-frame, an in-frame change of at least 193 residues, or RNase IIIb disruption.
• Alternatively, a validated in vitro pre-miRNA cleavage assay with positive and negative controls is needed to assess production of 5p and 3p microRNAs.

Sources

Reasoning

The DICER1 VCEP specification requires phenotype points from qualifying unrelated probands for PS4. The evidence bundle contains no affected-proband observations, phenotype-point assignments, case-control enrichment data, or eligible tumor data for this exact variant.

Rule

DICER1 VCEP PS4: qualifying unrelated probands contribute up to 1 phenotype point each; Supporting 1–1.5 points, Moderate 2–3.5 points, Strong ≥4 points.

Evidence considered

• The DICER1 VCEP specification applies PS4 at Supporting for 1–1.5 phenotype points, Moderate for 2–3.5 points, and Strong for 4 or more points; no phenotype points or qualifying probands are provided in this case bundle.
• The only literature record supplied is PMID:25741868; its precomputed extraction reports that neither DICER1 nor c.4206+11_4206+13del is mentioned, so it provides no case evidence for PS4.

Still missing

• Qualifying unrelated proband observations with DICER1 phenotype-point assignments are not available.
• No case-control enrichment estimate or exact-variant affected-versus-control dataset is available.

Sources

Reasoning

The DICER1 VCEP applies PP1 according to the number of informative meioses, but the case-evidence bundle contains no affected relatives, genotype-positive relatives, pedigree, segregation observations, or meiosis count. PP1 therefore cannot be assessed.

Rule

DICER1 VCEP PP1: Strong for >=7 meioses across >=2 families; Moderate for 5-6 meioses across >=1 family; Supporting for 3-4 meioses across >=1 family.

Evidence considered

• The governing ClinGen DICER1 VCEP specifies PP1 as Strong for >=7 meioses across >=2 families, Moderate for 5-6 meioses across >=1 family, and Supporting for 3-4 meioses across >=1 family.
• The consolidated case-evidence bundle provides no family segregation data or meiosis count for this variant.

Still missing

• Pedigree identifying informative relatives and their relationship to the proband
• Phenotype status of each relative, with high- or moderate-specificity DICER1-related findings where applicable
• Genotype status of each relative for NM_177438.3:c.4206+11_4206+13del
• Informative meiosis count and family count

Sources

Reasoning

PP3_Supporting is not applied. This intronic variant has a low SpliceAI maximum delta score (0.012), which does not support a splice effect, and no MaxEntScan result is available to establish the VCEP-required predictor concordance for an intronic/splicing variant.

Rule

DICER1 VCEP PP3_Supporting: for splicing variants, concordance of MaxEntScan and SpliceAI.

Evidence considered

• The DICER1 VCEP specifies PP3_Supporting for splicing variants only with concordance of MaxEntScan and SpliceAI, and directs assessment of all variants by both predictors for de novo and cryptic splice sites.
• SpliceAI Lookup reports DS_AG 0.012, DS_AL 0.001, DS_DG 0.004, and DS_DL 0.001 (maximum delta 0.012), reported as no significant splice impact.

Still missing

• MaxEntScan assessment for the exact normalized variant, including evaluation for any de novo or cryptic splice-site effect, is not available.

Sources

Reasoning

The DICER1 VCEP PP4 rule requires tumor testing in a DICER1-associated neoplasm showing retention of the germline variant and a previously reported somatic RNase IIIb hotspot second hit, with no additional somatic DICER1 non-hotspot loss-of-function variant. No patient phenotype, tumor sequencing, germline-retention result, or somatic second-hit data are supplied.

Rule

DICER1 VCEP PP4: in a DICER1-associated neoplasm, a somatic RNase IIIb hotspot second hit and retention of the germline variant are required, with no additional somatic DICER1 non-hotspot loss-of-function variant.

Evidence considered

• The DICER1 VCEP-specific PP4 rule is tumor-based rather than a general phenotype-specificity rule and requires the defined somatic second-hit pattern; the bundle contains none of those required observations.
• COSMIC reports no prior somatic-cancer report for this variant, which does not establish or exclude the required tumor result in the tested individual.

Still missing

• A DICER1-associated tumor type and tumor-sequencing results are not available.
• Evidence of retention of the germline variant and an eligible somatic RNase IIIb hotspot second hit without an additional somatic DICER1 non-hotspot loss-of-function variant is not available.

Sources

Reasoning

No validated benign functional study for NM_177438.3:c.4206+11_4206+13del was identified. Under the DICER1 VCEP specification, BS3 requires repeated RNA evidence of no splicing impact for intronic variants, or a controlled in vitro cleavage assay demonstrating production of both 5p and 3p microRNAs; neither is available in the case evidence.

Evidence considered

• The ClinGen DICER1 and miRNA-Processing Gene Expert Panel specification, version 1.4, defines BS3 Strong for intronic or synonymous variants with no splicing impact observed by RNA assay more than once, and BS3 Supporting for a controlled cleavage assay showing production of both 5p and 3p microRNAs.
• The case bundle contains no variant-specific RNA assay or cleavage-assay result. SpliceAI prediction of no significant splice impact is computational evidence and is insufficient by itself for BS3.

Still missing

• At least repeated variant-specific RNA assay evidence showing no splicing impact is needed for BS3 Strong under the DICER1 VCEP rule.
• A controlled in vitro cleavage assay demonstrating production of both 5p and 3p microRNAs from pre-miRNA could support BS3 Supporting.

Sources

Reasoning

The DICER1 VCEP requires phenotype-positive, genotype-negative first-, second-, or third-degree relatives for BS4. The case-evidence bundle contains no phenotype-positive relatives, genotype-negative relatives, relationship information, or segregation testing results. BS4 therefore cannot be assessed.

Rule

DICER1 VCEP BS4: Strong when phenotype-positive first-, second-, or third-degree relatives with high- or moderate-specificity phenotype are genotype-negative.

Evidence considered

• The governing ClinGen DICER1 VCEP specifies BS4 as Strong when high- or moderate-specificity phenotype-positive first-, second-, or third-degree relatives are genotype-negative for the variant.
• The consolidated case-evidence bundle provides no non-segregation observations or relevant relative testing for this variant.

Still missing

• Identification of phenotype-positive first-, second-, or third-degree relatives
• Objective high- or moderate-specificity phenotype documentation for those relatives
• Validated negative genotype results for the variant in those relatives
• Relationship degree and assessment of whether the relatives are informative

Sources

Reasoning

The DICER1 VCEP permits BP2 at Supporting strength for at least one observation in trans with a P/LP DICER1 variant, or at least three observations in cis or with phase unknown involving two or more different P/LP DICER1 variants. The case bundle contains no affected-proband observations, second DICER1 variant, phase data, parental testing, or other inheritance evidence establishing any BP2-eligible observation.

Rule

Supporting: at least one observation in trans with a P/LP DICER1 variant, or at least three observations in cis or phase unknown with two or more different P/LP DICER1 variants.

Evidence considered

• The DICER1 VCEP BP2 rule requires at least one trans observation with a P/LP DICER1 variant, or at least three cis or phase-unknown observations involving two or more different P/LP DICER1 variants.
• The consolidated case-evidence bundle provides no proband-level allelic, phase, parental, or affected-family-member data relevant to BP2.
• The only paper extraction in the bundle is general ACMG/AMP guidance and does not mention DICER1, the exact variant, or any allelic observation; it therefore does not provide BP2 evidence.

Still missing

• No documented co-occurring P/LP DICER1 variant in the same individual.
• No phase information establishing cis or trans configuration.
• No parental or offspring testing information to determine phase.
• No qualifying set of three observations in cis or phase unknown involving at least two different P/LP DICER1 variants.

Sources

Reasoning

BP4_Supporting is not applied. Although SpliceAI predicts no significant splice impact (maximum delta 0.012), the DICER1 VCEP requires concordance of MaxEntScan and SpliceAI for intronic variants; the MaxEntScan result is unavailable.

Rule

DICER1 VCEP BP4_Supporting: for synonymous/intronic/non-coding variants, concordance of MaxEntScan and SpliceAI.

Evidence considered

• The DICER1 VCEP specifies BP4_Supporting for synonymous, intronic, and non-coding variants only with concordance of MaxEntScan and SpliceAI. The VCEP notes that SpliceAI alone is used for native consensus-site impact only when a variant lies outside the MaxEntScan validation threshold; this does not remove the instruction to assess de novo and cryptic sites with both predictors.
• SpliceAI Lookup reports DS_AG 0.012, DS_AL 0.001, DS_DG 0.004, and DS_DL 0.001 (maximum delta 0.012), reported as no significant splice impact.

Still missing

• MaxEntScan assessment for the exact normalized variant, including evaluation for any de novo or cryptic splice-site effect, is not available.

Sources

Reasoning

BP7_Supporting is not applied. The variant is intronic at +11, a position class eligible for BP7 under the DICER1 VCEP, but the VCEP explicitly requires BP4 first; BP4 cannot be assessed without the required MaxEntScan result.

Rule

DICER1 VCEP BP7_Supporting: intronic variant at or beyond +7 to -21; caveat, BP4 must be met.

Evidence considered

• The DICER1 VCEP allows BP7 for an intronic variant at or beyond +7 to -21 positions, with the explicit caveat that the variant must meet BP4.
• The submitted and normalized transcript description is NM_177438.3:c.4206+11_4206+13del, placing the deletion at intronic +11 through +13.

Still missing

• A complete BP4 assessment requires MaxEntScan evaluation for the exact normalized variant; BP7 cannot be applied until BP4 is met.

Sources