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LYFE SCIENCES
Project: HERA
NM_177438.3:c.4680G>A
p.Ala1560=  ·  DICER1
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Classification rationale
1

The DICER1 c.4680G>A (p.Ala1560=) variant has been reported in ClinVar with benign classifications from multiple clinical laboratories.

clinvar ↗
2

This variant is common in population databases, including gnomAD v4.1 with total allele frequency 0.00631 and African/African American allele frequency 0.11919, which is well above the DICER1 BA1 threshold of 0.003; gnomAD-Canada also shows allele frequency 0.00863 with 11 homozygotes.

cspec ↗ gnomad_v4 ↗ gnomad_canada ↗
3

Computational data do not support a splice-disrupting effect, with SpliceAI max delta score 0.01, and the REVEL score is 0.07.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
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Gaps remaining
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Rule
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Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.0117076; MAF= 1.17076%, 3311/282808 alleles, homozygotes = 195) and has highest observed frequency in the African/African American population (AF= 0.122266; MAF= 12.22658%, 3052/24962 alleles, homozygotes = 193); grpmax FAF= 0.1183.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.00631039; MAF= 0.63104%, 10186/1614164 alleles, homozygotes = 596) and has highest observed frequency in the African/African American population (AF= 0.11919; MAF= 11.91905%, 8940/75006 alleles, homozygotes = 577); grpmax FAF= 0.117124.
gnomAD CanadaThis variant is present in gnomAD-Canada v1.0 (AF= 0.00863286; MAF= 0.86329%, 159/18418 alleles, homozygotes = 11) and has highest observed frequency in the afr population (AF= 0.140196; grpmax FAF95= 0.121485).
gnomAD v2 ↗ gnomAD v4 ↗ gnomAD 🇨🇦 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Benign (11 clinical laboratories) and as benign (1 clinical laboratory). (ClinVarID = 261925)
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.07.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueA1560
Hotspots ↗