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DICER1
Final classification
VUS
DICER1 c.1282G>C · p.Glu428Gln
DICER1

NM_177438.2:c.1282G>C (p.Glu428Gln) is a missense variant in exon 8 of DICER1, located in the N-terminal DExD helicase domain, outside the RNase IIIb domain and metal ion-binding hotspot residues.

Gene
DICER1
Transcript
NM_177438.2
HGVS · transcript:coding
NM_177438.2:c.1282G>C
Consequence
N/A
GRCh38
chr14:95124290 C>G
GRCh37
chr14:95590627 C>G
Basis ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4 v1.4 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) = 0 points, which maps to VUS.
ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4 v1.4 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) = 0 points, which maps to VUS.
Classification rationale
PM2 BP4 VUS
DICER1 c.1282G>C

NM_177438.2:c.1282G>C (p.Glu428Gln) is a missense variant in exon 8 of DICER1, located in the N-terminal DExD helicase domain, outside the RNase IIIb domain and metal ion-binding hotspot residues.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the DICER1 VCEP PM2_Supporting criterion (AF < 0.000005).2 Computational evidence suggests a benign effect: REVEL score is 0.186 (< 0.500), BayesDel score is -0.262, and SpliceAI predicts no splicing impact (max delta = 0.00), meeting the DICER1 VCEP BP4_Supporting criterion.3 The variant has been observed once in somatic cancers (COSMIC COSV100602630) but has not been reported in ClinVar or the germline literature.4 No functional data, de novo observations, family segregation data, or tumor sequencing data are available to assess PS3, PS2, PP1, or PP4. Under the DICER1 VCEP v1.4 Tavtigian point-based system: PM2_Supporting (+1) + BP4_Supporting (-1) = 0 points, classifying this variant as a Variant of Uncertain Significance.5

PM2 + BP4 VUS
Gene diagram · NM_177438.2 · variants mapped to exon structure
DICER1 NM_177438.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 15 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_177438.2:c.1282G>C is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with allele frequency < 0.000005, meeting the DICER1 VCEP PM2_Supporting threshold.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0.
BP4 supporting Benign
The DICER1 VCEP BP4 rule requires REVEL < 0.500 and agreement in splicing predictors that no splicing effects are predicted. REVEL is 0.186 (< 0.500) and SpliceAI predicts no splicing impact (max delta = 0.00). BayesDel (-0.262) also supports a benign computational profile.
REVEL score 0.186 (< 0.500 threshold).SpliceAI max delta 0.00 (no splicing effect).BayesDel score -0.262 (benign-leaning).
Assessed · not applied
Pathogenic
PS1 PS1 requires a different nucleotide change resulting in the same amino acid substitution (p.Glu428Gln) classified as pathogenic by the ClinGen DICER1 VCEP.
PS2 No de novo data are available for this variant.
PS3 No functional data exist for NM_177438.2:c.1282G>C.
PS4 No clinical phenotype data from unrelated probands are available for this variant.
PM1 The DICER1 VCEP defines PM1 for missense variants at metal ion-binding residues (p.S1344, E1705, D1709, D1713, G1809, D1810, E1813; moderate) or within the RNase IIIb domain (p.Y1682–S1846; supporting).
PM5 PM5 requires a different missense variant at the same residue (p.Glu428) classified as pathogenic by the ClinGen DICER1 VCEP.
PP1 No cosegregation data are available.
PP3 The DICER1 VCEP requires REVEL ≥ 0.750 for PP3_Supporting in missense variants.
PP4 No somatic tumor testing data are available to evaluate for an RNase IIIb hotspot second hit with retention of the germline variant.
Benign
BA1 BA1 requires allele frequency > 0.003 (0.3%) in gnomAD subpopulations with >2,000 alleles tested and ≥5 alleles present.
BS1 BS1 requires allele frequency > 0.0003 (0.03%) in gnomAD subpopulations with >2,000 alleles tested and ≥5 alleles present.
BS2 No data are available regarding tumor-free females through age 50 or homozygosity observations for this variant.
BS3 No functional data are available to evaluate a benign effect.
BS4 No family segregation data are available.
BP2 No data are available regarding observations of this variant in trans with a known P/LP DICER1 variant or in cis/phase unknown with multiple P/LP DICER1 variants.
N/A · 11 PVS1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.186. BayesDel score = -0.262519.
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 previously been reported in somatic cancers (COSMIC; COSV100602630, n = 1 times).
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