DICER1 c.1510-4dup, p.?

Reasoning

The governing ClinGen DICER1 VCEP specification requires BA1 at frequency >0.003 in a gnomAD subpopulation with >2,000 alleles tested and at least 5 variant alleles. Using the VCEP's instruction to use the most recent and comprehensive gnomAD version, gnomAD v4.1 reports the variant at AF 0.0131239 in the African/African American subpopulation (935/71,244 alleles; 3 homozygotes), exceeding the BA1 threshold with ample allele count.

Rule

ClinGen DICER1 VCEP v1.4 BA1: frequency >0.003 in a gnomAD subpopulation; subpopulation must have >2,000 alleles tested and at least 5 alleles present.

Evidence considered

• ClinGen DICER1 VCEP version 1.4 specifies BA1 as frequency >0.003 in a gnomAD subpopulation with >2,000 alleles tested and at least 5 alleles present, and directs users to use the most recent/most comprehensive gnomAD version.
• gnomAD v4.1 reports AF 0.0131239 in the African/African American subpopulation, corresponding to 935 of 71,244 alleles and 3 homozygotes; this exceeds the VCEP BA1 threshold and satisfies the subpopulation sample requirements.

Sources

Reasoning

The governing ClinGen DICER1 VCEP specification requires BS1 at frequency >0.0003 in a gnomAD subpopulation with >2,000 alleles tested and at least 5 variant alleles. gnomAD v4.1 reports AF 0.0131239 in the African/African American subpopulation (935/71,244 alleles; 3 homozygotes), which exceeds the BS1 threshold and meets the sample requirements.

Rule

ClinGen DICER1 VCEP v1.4 BS1: frequency >0.0003 in a gnomAD subpopulation; subpopulation must have >2,000 alleles tested and at least 5 alleles present.

Evidence considered

• ClinGen DICER1 VCEP version 1.4 specifies BS1 as frequency >0.0003 in a gnomAD subpopulation; the subpopulation must have >2,000 alleles tested and at least 5 alleles present.
• gnomAD v4.1 reports AF 0.0131239 in the African/African American subpopulation, corresponding to 935 of 71,244 alleles and 3 homozygotes; this exceeds the VCEP BS1 threshold and satisfies the subpopulation sample requirements.

Sources

Reasoning

The governing ClinGen DICER1 VCEP permits BS2 Supporting for 2 or more observations of homozygosity in individuals lacking clinical information. gnomAD v4.1 reports 6 homozygotes for this variant overall, including 3 in the African/African American subpopulation and additional homozygotes in other subpopulations. These gnomAD observations provide at least two homozygous observations, but the database does not establish that the individuals are clinically healthy, so the VCEP's Supporting rather than Strong homozygosity rule applies.

Rule

ClinGen DICER1 VCEP v1.4 BS2 Supporting: 2 or more observations of homozygosity in individuals lacking clinical information.

Evidence considered

• ClinGen DICER1 VCEP version 1.4 specifies BS2 Supporting for 2 or more observations of homozygosity in individuals lacking clinical information; Strong requires either 2 or more homozygous observations in healthy individuals or confirmed parental testing, or the specified tumor-free female cohorts.
• gnomAD v4.1 reports total_hom 6 for the variant, including 3 homozygotes in the African/African American subpopulation; this meets the VCEP's minimum count for the Supporting homozygosity rule, while no clinical health status or parental confirmation is provided.

Sources

Reasoning

The governing ClinGen DICER1 VCEP requires PM2 Supporting when allele frequency is <0.000005 across gnomAD, with no more than one allele in any subpopulation and at least 20x coverage. The variant is common in gnomAD v4.1 (overall AF 0.00142555; 2,181/1,529,938 alleles; 6 homozygotes) and has 935 alleles in the African/African American subpopulation, so it fails the frequency, allele-count, and absence requirements. The gnomAD v2.1 non-cancer exome subset also reports AF 0.00205383 (411/200,114 alleles), which likewise cannot support PM2; the VCEP does not require that subset and directs use of the most recent comprehensive dataset.

Rule

ClinGen DICER1 VCEP v1.4 PM2 Supporting: allele frequency <0.000005 across gnomAD, with no more than one allele in any subpopulation and at least 20x coverage.

Evidence considered

• ClinGen DICER1 VCEP version 1.4 specifies PM2 Supporting as allele frequency <0.000005 across gnomAD, with no more than one allele in any subpopulation and at least 20x coverage, and states that the most recent/most comprehensive gnomAD version should generally be used.
• gnomAD v4.1 reports overall AF 0.00142555, with 2,181 of 1,529,938 alleles and 6 homozygotes; the African/African American subpopulation contains 935 variant alleles at AF 0.0131239.
• The gnomAD v2.1 non-cancer exome subset reports AF 0.00205383, or 411 of 200,114 exome alleles, with no homozygotes; this also exceeds the PM2 threshold by several orders of magnitude.

Sources

Reasoning

The DICER1 VCEP permits PS1 for a same-amino-acid change only when equivalent splicing is established, or for a non-canonical intronic variant at the same nucleotide when the comparator has equal or worse splicing impact; this variant is NM_177438.3:c.1510-4dupT with protein consequence p.? and SpliceAI max delta 0.016, but no pathogenic ClinGen DICER1 VCEP comparator at the same nucleotide or protein change is documented. Therefore PS1 cannot be adjudicated from the available evidence.

Rule

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

Evidence considered

• The DICER1 VCEP PS1 rule requires a same-amino-acid pathogenic comparison with no splicing difference, or a non-canonical intronic same-nucleotide comparison with equal or worse splicing impact.
• The evaluated variant is NM_177438.3:c.1510-4dupT and is normalized as NP_803187.1:p.?; SpliceAI maximum delta is 0.016.
• No qualifying pathogenic comparator is present in the collected PM5 comparator evidence.

Still missing

• A ClinGen DICER1 VCEP-pathogenic comparator at the same nucleotide or producing the same amino-acid change, with comparable splicing evidence, is not documented.

Sources

Reasoning

The DICER1 VCEP permits PS2 using de novo points when both maternity and paternity are confirmed and the patient has the disease without a family history, with strength determined by the point total. The available case evidence contains no proband-level parental testing, confirmed maternity or paternity, de novo observation, family-history assessment, or de novo point calculation for NM_177438.3:c.1510-4dup; therefore PS2 cannot be assessed.

Rule

De novo points should be tallied using the simplified table for tallying proband points. The DICER1 VCEP uses PS2 exclusively for de novo evidence; >=4 de novo points = Very Strong, >=2 but <4 = Strong, >=1 but <2 = Moderate, and >=0.5 but <1 = Supporting.

Evidence considered

• The DICER1 VCEP specifies PS2 as applicable when de novo evidence is supported by confirmed maternity and paternity and assigns Very Strong, Strong, Moderate, or Supporting strength at >=4, >=2 and <4, >=1 and <2, or >=0.5 and <1 de novo points, respectively.
• No proband-level parental testing, confirmed maternity or paternity, de novo observation, family-history assessment, or de novo point tally is documented in the supplied case evidence.

Still missing

• Documented proband phenotype and disease status
• Parental testing results for both biological parents
• Confirmation of maternity and paternity
• Family-history assessment
• De novo point calculation

Sources

Reasoning

The ClinGen DICER1 VCEP specification permits PS3 for variant-specific functional evidence of abnormal splicing or reduced DICER1 pre-miRNA cleavage, with Supporting strength requiring an in vitro cleavage assay showing failure or severe reduction in production of either 5p or 3p microRNAs and positive and negative controls. The available case evidence contains no variant-specific RNA assay, cleavage assay, assay controls, or quantitative functional result for NM_177438.3:c.1510-4dupT; SpliceAI prediction is computational evidence and cannot establish PS3.

Rule

RNA assay shows splicing impact that is out-of-frame, in-frame >=193 residues, or in-frame with RNase IIIb disruption (PS3_Moderate if PVS1_Strong is applied); or an in vitro cleavage assay shows failure or severely reduced capacity to produce either 5p or 3p microRNAs from a premiRNA with positive and negative controls.

Evidence considered

• The DICER1 VCEP PS3 rule covers RNA evidence of abnormal splicing or reduced DICER1 pre-miRNA cleavage; its Supporting rule requires failure or severe reduction in production of either 5p or 3p microRNAs with positive and negative controls.
• The case evidence reports only SpliceAI max delta 0.016, a computational prediction, and provides no variant-specific functional assay result or assay-control data.

Still missing

• Variant-specific RNA assay data showing the splicing consequence are unavailable.
• Variant-specific in vitro pre-miRNA cleavage data for 5p and 3p microRNA production are unavailable.
• Assay positive and negative controls and reproducibility information are unavailable.

Sources

Reasoning

The ClinGen DICER1 VCEP Version 1.4 defines PS4 by phenotype points: supporting requires 1–1.5 points, moderate requires 2–3.5 points, and strong requires ≥4 points. The available evidence does not provide phenotype-point assignments or a case-control enrichment analysis for this exact variant. General DICER1 cancer-predisposition references do not mention NM_177438.3:c.1510-4dup, so PS4 cannot be assessed.

Rule

ClinGen DICER1 VCEP Version 1.4 PS4: Supporting = 1–1.5 phenotype points; Moderate = 2–3.5 phenotype points; Strong = ≥4 phenotype points.

Evidence considered

• The DICER1 VCEP Version 1.4 PS4 rule assigns supporting strength at 1–1.5 phenotype points, moderate strength at 2–3.5 points, and strong strength at ≥4 points.
• The reviewed cancer-predisposition guidance discusses DICER1-associated tumors generally but does not report this exact variant or provide variant-specific enrichment data.

Still missing

• No variant-specific phenotype-point assignments or case-control enrichment data were found.

Sources

Reasoning

The DICER1 VCEP requires phenotype-positive relatives with high-, moderate-, or low-specificity phenotypes and assigns PP1 Supporting for 3–4 meioses, Moderate for 5–6 meioses, and Strong for >=7 meioses across >=2 families. The available case evidence contains no affected relatives, familial variant observations, segregation results, phenotype-specific relatives, family count, or meiosis count for NM_177438.3:c.1510-4dup; therefore PP1 cannot be assessed.

Rule

Phenotype-positive individuals should have high-, moderate-, or low-specificity phenotypes; do not apply PP1 for segregation with a single low-specificity phenotype across multiple individuals. 3–4 meioses across >=1 family = Supporting, 5–6 meioses across >=1 family = Moderate, and >=7 meioses across >=2 families = Strong.

Evidence considered

• The DICER1 VCEP requires phenotype-positive individuals and defines PP1 Supporting as 3–4 meioses across at least 1 family, Moderate as 5–6 meioses across at least 1 family, and Strong as >=7 meioses across at least 2 families.
• No familial segregation observations, affected relatives, relative phenotypes, family count, or meiosis count are documented in the supplied case evidence.

Still missing

• Family structure and relationship degrees
• Variant genotypes in relatives
• Phenotype status and specificity for each relative
• Number of informative meioses
• Number of informative families

Sources

Reasoning

The variant is an intronic splice-region variant, so PP3 is in scope through the splicing-prediction path. The DICER1 VCEP requires concordance of MaxEntScan and SpliceAI for splicing variants. SpliceAI predicts minimal splice impact with a maximum delta score of 0.016, below the generic supporting threshold of 0.2 and the moderate threshold of 0.5, but no MaxEntScan result is available. Because the governing VCEP rule requires both predictors for this position, PP3 cannot be adjudicated.

Rule

DICER1 VCEP PP3: For splicing variants, concordance of MaxEntScan and SpliceAI.

Evidence considered

• The ClinGen DICER1 VCEP specifies PP3 supporting evidence for splicing variants when MaxEntScan and SpliceAI are concordant for predicted splicing effects.
• SpliceAI reports DS_AG 0.016, DS_AL 0.013, DS_DG 0.000, DS_DL 0.003, and maximum delta score 0.016 for NM_177438.3:c.1510-4dup.
• The supplied generic SpliceAI calibration defines PP3 supporting at max delta >=0.2 and PP3 moderate at >=0.5; the score 0.016 does not meet either threshold, but the VCEP-specific concordance requirement remains unresolved without MaxEntScan.

Still missing

• MaxEntScan result for the c.1510-4 splice-region variant is unavailable; VCEP-required predictor concordance cannot be established.

Sources

Reasoning

The ClinGen DICER1 VCEP Version 1.4 specifies PP4 as supporting only when tumor testing in a proband with the germline variant shows a previously reported somatic RNase IIIb hotspot second hit, retention of the germline variant, and no additional somatic DICER1 loss-of-function variants. COSMIC reports this exact variant twice in somatic cancers, but provides no tumor-level hotspot second-hit, germline-retention, or exclusion-of-additional-LOF data. Therefore the VCEP PP4 rule cannot be assessed.

Rule

ClinGen DICER1 VCEP Version 1.4 PP4: supporting when tumor testing identifies a previously reported somatic RNase IIIb hotspot second hit, retains the germline DICER1 variant, and reveals no additional somatic DICER1 loss-of-function variants; not applicable if additional non-hotspot DICER1 variants are present.

Evidence considered

• The DICER1 VCEP Version 1.4 PP4 rule requires a known RNase IIIb hotspot somatic second hit, retention of the germline variant, and no additional somatic DICER1 loss-of-function variants.
• COSMIC records NM_177438.3:c.1510-4dup as COSV104413821 with a somatic count of 2, without the tumor-level details required by the VCEP PP4 rule.

Still missing

• Tumor-level evidence is missing for a qualifying RNase IIIb hotspot second hit, germline-variant retention, and absence of additional somatic DICER1 loss-of-function variants.

Sources

Reasoning

The ClinGen DICER1 VCEP specification permits BS3 for variant-specific functional evidence of no splicing impact or preserved DICER1 pre-miRNA cleavage. Strong strength requires an RNA assay showing no splicing impact, observed more than once; Supporting strength requires an in vitro cleavage assay demonstrating production of both 5p and 3p microRNAs from a pre-miRNA with positive and negative controls. The available case evidence contains no variant-specific RNA assay, cleavage assay, assay controls, replication, or quantitative functional result for NM_177438.3:c.1510-4dupT, so benign functional evidence cannot be established.

Rule

For intronic or synonymous variants, no splicing impact observed via RNA assay (should be observed more than once); or an in vitro cleavage assay must demonstrate the variant produces both 5p and 3p microRNAs from a pre-miRNA with positive and negative controls also performed.

Evidence considered

• The DICER1 VCEP BS3 rule requires either replicated RNA evidence of no splicing impact for Strong strength or an in vitro cleavage assay showing production of both 5p and 3p microRNAs with positive and negative controls for Supporting strength.
• The case evidence reports only SpliceAI max delta 0.016, a computational prediction, and provides no variant-specific functional assay result, replication, or assay-control data.

Still missing

• Variant-specific RNA assay data demonstrating absence of splicing impact are unavailable.
• Variant-specific cleavage data demonstrating production of both 5p and 3p microRNAs are unavailable.
• Assay positive and negative controls, replication, and reproducibility information are unavailable.

Sources

Reasoning

The DICER1 VCEP permits BS4 at Strong strength when phenotype-positive first-, second-, or third-degree relatives of the proband are genotype-negative for the variant. The available case evidence contains no documented affected relatives, relative genotypes, relationship degrees, phenotype specificity, or non-segregation observation for NM_177438.3:c.1510-4dup; therefore BS4 cannot be assessed.

Rule

Family members should be phenotype-positive with a high- or moderate-specificity phenotype and genotype-negative for the variant; eligible relatives are first-, second-, or third-degree relatives of the proband.

Evidence considered

• The DICER1 VCEP defines BS4 at Strong strength as phenotype-positive, genotype-negative first-, second-, or third-degree relatives of the proband, with high- or moderate-specificity phenotypes.
• No phenotype-positive genotype-negative relatives, relationship degrees, relative genotypes, or non-segregation observation are documented in the supplied case evidence.

Still missing

• Phenotype-positive relatives with high- or moderate-specificity phenotypes
• Relative relationship degrees
• Genotype results showing absence of the variant
• Assessment for phenocopies or another pathogenic variant

Sources

Reasoning

The DICER1 VCEP BP2 rule requires at least one observation in trans with a P/LP DICER1 variant, or at least three observations in cis or phase unknown involving two or more different P/LP DICER1 variants. The available case evidence contains no documented affected-proband observation, second P/LP DICER1 variant, cis/trans phase, or qualifying co-occurrence count, so BP2 cannot be assessed.

Rule

Supporting: ≥1 observation in trans with a P/LP DICER1 variant, or ≥3 observations in cis or phase unknown with 2+ different P/LP DICER1 variants.

Evidence considered

• The DICER1 VCEP Version 1.4 defines BP2 as supporting for 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.
• No qualifying affected-proband co-occurrence, second P/LP DICER1 variant, phase assignment, or observation count is documented in the available case evidence.

Still missing

• Documented co-occurrence of NM_177438.3:c.1510-4dup with another P/LP DICER1 variant in an affected proband
• Validated cis/trans phase or enough independent observations to meet the VCEP BP2 threshold

Sources

Reasoning

The variant is an intronic splice-region variant, so BP4 is in scope through the splicing-prediction path. The DICER1 VCEP requires concordance of MaxEntScan and SpliceAI showing no predicted splicing effect. SpliceAI predicts minimal splice impact with a maximum delta score of 0.016, below the generic supporting threshold of 0.1, but no MaxEntScan result is available. Because the governing VCEP rule requires both predictors for this position, BP4 cannot be adjudicated.

Rule

DICER1 VCEP BP4: For synonymous/intronic/non-coding variants, concordance of MaxEntScan and SpliceAI.

Evidence considered

• The ClinGen DICER1 VCEP specifies BP4 supporting evidence for intronic variants when MaxEntScan and SpliceAI are concordant that no splicing effects are predicted.
• SpliceAI reports DS_AG 0.016, DS_AL 0.013, DS_DG 0.000, DS_DL 0.003, and maximum delta score 0.016 for NM_177438.3:c.1510-4dup.
• The supplied generic SpliceAI calibration defines BP4 supporting at max delta <=0.1; the score 0.016 meets that numerical threshold, but the VCEP-specific concordance requirement remains unresolved without MaxEntScan.

Still missing

• MaxEntScan result for the c.1510-4 splice-region variant is unavailable; VCEP-required predictor concordance cannot be established.

Sources