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DICER1
Final classification
Benign
DICER1 c.2997T>G · p.Leu999=
DICER1

NM_177438.3:c.2997T>G (p.Leu999=) is a synonymous variant in exon 19 of DICER1. It is present at high frequency in gnomAD v4.1 with an overall allele frequency of 0.31% (5007/1613832 alleles) and 121 homozygotes. The highest subpopulation frequency is 5.69% in African/African American individuals (4272/75026 alleles, 116 homozygotes), exceeding the VCEP BA1 stand-alone benign threshold of >0.3%.

Gene
DICER1
Transcript
NM_177438.3
HGVS · transcript:coding
NM_177438.3:c.2997T>G
Consequence
N/A
GRCh38
chr14:95105774 A>C
GRCh37
chr14:95572111 A>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: BA1 stand-alone benign (-8) + BS1 strong benign (-4) + BS2 supporting benign (-1) + BP4 supporting benign (-1) + BP7 supporting benign (-1) = -15 points, which maps to 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: BA1 stand-alone benign (-8) + BS1 strong benign (-4) + BS2 supporting benign (-1) + BP4 supporting benign (-1) + BP7 supporting benign (-1) = -15 points, which maps to Benign.
Classification rationale
BA1BS1BS2BP4BP7 Benign
DICER1 c.2997T>G

NM_177438.3:c.2997T>G (p.Leu999=) is a synonymous variant in exon 19 of DICER1. It is present at high frequency in gnomAD v4.1 with an overall allele frequency of 0.31% (5007/1613832 alleles) and 121 homozygotes. The highest subpopulation frequency is 5.69% in African/African American individuals (4272/75026 alleles, 116 homozygotes), exceeding the VCEP BA1 stand-alone benign threshold of >0.3%.1 BA1 (Stand-Alone Benign) is met: the African/African American subpopulation allele frequency of 5.69% exceeds the 0.3% threshold with >2000 alleles tested and ≥5 alleles present. A frequency of this magnitude is incompatible with a highly penetrant autosomal dominant tumor predisposition disorder.2 BS1 (Strong Benign) is independently met at the >0.03% threshold in the same subpopulation, subsumed by the stronger BA1 evidence.3 BS2_Supporting is met: 121 homozygous individuals are reported in gnomAD v4.1, satisfying the VCEP threshold of ≥2 homozygotes in individuals lacking clinical information.4 BP4_Supporting is met: SpliceAI predicts no splicing impact for this synonymous variant (max delta score = 0.03).5 BP7_Supporting is met: the variant is a synonymous change (p.Leu999=) and meets BP4, satisfying the DICER1 VCEP BP7 requirements.6 This variant has been classified as Benign by 10 clinical laboratories in ClinVar (VariationID: 261920), consistent with the population frequency evidence.7 No publications among the seven reviewed (PMID:25741868, 26467025, 24493721, 29474644, 24761742, 25394175, 28492532) specifically mention NM_177438.3:c.2997T>G or p.Leu999=. All are methodology, guideline, or gene-level review papers without variant-specific evidence.8 Under the Tavtigian point-based system (DICER1 VCEP v1.4.0): BA1 = -8 points. BS2_Supporting = -1 point. BP4_Supporting = -1 point. BP7_Supporting = -1 point. Total = -11 points. Classification: Benign (≤ -7).9

BA1 + BS1 + BS2 + BP4 + BP7 Benign
Gene diagram · NM_177438.3 · variants mapped to exon structure
DICER1 NM_177438.3
Fetching transcript structure from UCSC…
Applied criteria · 5 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= 0.00310255; MAF= 0.31026%, 5007/1613832 alleles, homozygotes = 121) and has highest observed frequency in the African/African American population (AF= 0.0569403; MAF= 5.69403%, 4272/75026 alleles, homozygotes = 116); grpmax FAF= 0.0555142.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.00563595; MAF= 0.56359%, 1593/282650 alleles, homozygotes = 38) and has highest observed frequency in the African/African American population (AF= 0.05716; MAF= 5.71600%, 1425/24930 alleles, homozygotes = 38); grpmax FAF= 0.0559887.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.0036377456835704203, 67/18418 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.31% · 5007 / 1,613,832
      121 hom · FAF 5.6%
      African/African American
      4272 / 75,026
      5.7%
      116 hom
      Remaining individuals
      259 / 62,496
      0.41%
      4 hom
      Admixed American
      233 / 60,030
      0.39%
      Middle Eastern
      20 / 6,060
      0.33%
      1 hom
      European (non-Finnish)
      216 / 1,179,712
      0.018%
      South Asian
      7 / 91,072
      0.0077%
      + 4 not observed (European (Finnish), Amish, East Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.56% · 1593 / 282,650
      38 hom · FAF 5.6%
      African/African American
      1425 / 24,930
      5.7%
      38 hom
      Admixed American
      109 / 35,434
      0.31%
      Remaining individuals
      17 / 7,208
      0.24%
      European (non-Finnish)
      40 / 129,032
      0.031%
      South Asian
      2 / 30,606
      0.0065%
      + 3 not observed (Ashkenazi Jewish, East Asian, European (Finnish))
      gnomAD Canada 🇨🇦
      0.36% · 67 / 18,418
      0 hom · FAF 4.3%
      African/African American
      55 / 1,020
      5.4%
      Middle Eastern
      1 / 144
      0.69%
      Latino/Admixed American
      5 / 838
      0.6%
      Remaining individuals
      5 / 1,138
      0.44%
      European (non-Finnish)
      1 / 11,738
      0.0085%
      + 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (9 clinical laboratories) and as benign (1 clinical laboratory). (ClinVarID = 261920)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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 · 7 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
      29474644 ↗ DICER1 Mutations Are Frequent in Adolescent-Onset Papillary Thyroid Carcinoma. CLINVAR
      24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. 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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR