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DICER1
Final classification
Likely Benign
DICER1 c.4199A>G · p.Asp1400Gly
DICER1

NM_177438.2:c.4199A>G (p.Asp1400Gly) is a missense variant in exon 22 of DICER1.

Gene
DICER1
Transcript
NM_177438.2
HGVS · transcript:coding
NM_177438.2:c.4199A>G
Consequence
N/A
GRCh38
chr14:95099787 T>C
GRCh37
chr14:95566124 T>C
Basis ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4.0 v1.4.0 point-based framework: BP4 supporting (-1) + BP6 supporting benign (-1) = -2 points, which maps to Likely Benign.
ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4.0 v1.4.0 point-based framework: BP4 supporting (-1) + BP6 supporting benign (-1) = -2 points, which maps to Likely Benign.
Classification rationale
BP4BP6 Likely Benign
DICER1 c.4199A>G

NM_177438.2:c.4199A>G (p.Asp1400Gly) is a missense variant in exon 22 of DICER1. This variant is present in gnomAD v4.1 at an allele frequency of 4.71e-05 (76/1,612,760 alleles, 0 homozygotes), with a grpmax filtering allele frequency of 4.511e-05. It has been observed across multiple subpopulations, including 7 alleles in the South Asian population (AF=7.69e-05). These frequencies exceed the DICER1 VCEP PM2_Supporting threshold of <5e-06.1 This variant has been reported in ClinVar as Likely Benign following review by the ClinGen DICER1 and miRNA-Processing Gene Variant Curation Expert Panel (ClinVar Variation ID: 412173). Individual clinical laboratory submissions include Uncertain Significance (4 laboratories) and Likely Benign (2 laboratories).2 In silico predictors support a benign interpretation: REVEL score is 0.142, well below the DICER1 VCEP BP4_Supporting threshold of <0.500. SpliceAI predicts no splicing impact (max delta = 0.12). These findings meet BP4_Supporting per DICER1 VCEP criteria.3 The variant has been observed in two siblings with pleuropulmonary blastoma (Leckey et al. 2019, PMID:30665929). However, both siblings also carried a pathogenic DICER1 splice variant (c.2437-2A>G), and the authors explicitly state that c.4199A>G 'has not been associated with DICER1-associated phenotypic features.' In silico algorithms reportedly suggest the variant 'is likely to be tolerated.' No functional studies have been performed.4 Residue Asp1400 lies outside the RNase IIIb domain (p.Y1682–S1846) and is not one of the seven metal ion-binding residues defined by the DICER1 VCEP for PM1. No pathogenic variant at the same residue is known for PS1 or PM5 application. No functional, segregation, de novo, or case-control data support application of any pathogenic criterion.5 Applying the DICER1 VCEP (version 1.4.0) point-based Tavtigian framework: only BP4_Supporting (−1 point) is met. All other applicable criteria are not met. Total point value = −1, which falls within the Uncertain Significance range (Rule 3: ≥−1 and ≤5).6

BP4 + BP6 Likely Benign
6 cspec ↗final_classification_framework
Gene diagram · NM_177438.2 · variants mapped to exon structure
DICER1 NM_177438.2
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.71242e-05; MAF= 0.00471%, 76/1612760 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 7.68673e-05; MAF= 0.00769%, 7/91066 alleles, homozygotes = 0); grpmax FAF= 4.511e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 2.79682e-05; MAF= 0.00280%, 7/250284 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 9.92457e-05; MAF= 0.00992%, 1/10076 alleles, homozygotes = 0); grpmax FAF= 1.687e-05.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0047% · 76 / 1,612,760
      0 hom · FAF 0.0045%
      South Asian
      7 / 91,066
      0.0077%
      European (non-Finnish)
      66 / 1,179,824
      0.0056%
      Ashkenazi Jewish
      1 / 29,588
      0.0034%
      Remaining individuals
      2 / 62,450
      0.0032%
      + 6 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, African/African American)
      gnomAD v2.1
      0.0028% · 7 / 250,284
      0 hom · FAF 0.0017%
      Ashkenazi Jewish
      1 / 10,076
      0.0099%
      European (non-Finnish)
      5 / 113,570
      0.0044%
      South Asian
      1 / 30,606
      0.0033%
      + 5 not observed (African/African American, Admixed American, East Asian, European (Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (4 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Likely Benign by ClinGen DICER1 and miRNA-Processing Gene Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 412173)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.12). REVEL score = 0.142. BayesDel score = -0.0837422.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. DICER1, an endoribonuclease, is altered in various cancer types.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      30665929 ↗ Novel intronic DICER1 variation associated with pleuropulmonary blastoma in two siblings. CLINVAR
      31275557 ↗ Pan-cancer repository of validated natural and cryptic mRNA splicing mutations. CLINVAR
      24761742 ↗ DICER1-Related Tumor Predisposition. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      29641532 ↗ Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR