The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_177438.3(DICER1):c.5486C>G (p.Thr1829Arg)

CA390864547

1513387 (ClinVar)

Gene: DICER1
Condition: DICER1-related tumor predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 5add8d04-86d5-4684-974e-be9c466316da
Approved on: 2025-08-26
Published on: 2025-09-19

HGVS expressions

NM_177438.3:c.5486C>G
NM_177438.3(DICER1):c.5486C>G (p.Thr1829Arg)
NC_000014.9:g.95091244G>C
CM000676.2:g.95091244G>C
NC_000014.8:g.95557581G>C
CM000676.1:g.95557581G>C
NC_000014.7:g.94627334G>C
NG_016311.1:g.71179C>G
ENST00000529720.2:c.5486C>G
ENST00000531162.7:c.5486C>G
ENST00000674628.2:c.5486C>G
ENST00000675540.2:c.*2136C>G
ENST00000696733.1:c.*108C>G
ENST00000696734.1:c.*141C>G
ENST00000696735.1:n.2473C>G
ENST00000696736.1:c.5486C>G
ENST00000696920.1:n.5749C>G
ENST00000696921.1:n.6592C>G
ENST00000696922.1:n.8417C>G
ENST00000696923.1:c.*141C>G
ENST00000696924.1:c.*108C>G
ENST00000696925.1:n.8417C>G
ENST00000343455.8:c.5486C>G
ENST00000393063.6:c.5486C>G
ENST00000526495.6:c.5486C>G
ENST00000556045.6:c.*203C>G
ENST00000675540.1:c.3231C>G
ENST00000675995.1:c.*3802C>G
ENST00000343455.7:c.5486C>G
ENST00000393063.5:c.5486C>G
ENST00000526495.5:c.5486C>G
ENST00000527414.5:c.5486C>G
ENST00000527416.2:n.79C>G
ENST00000527554.2:n.179C>G
ENST00000541352.5:c.5365-135C>G
ENST00000556045.5:c.2180C>G
NM_001195573.1:c.5365-135C>G
NM_001271282.2:c.5486C>G
NM_001291628.1:c.5486C>G
NM_030621.4:c.5486C>G
NM_177438.2:c.5486C>G
NM_001271282.3:c.5486C>G
NM_001291628.2:c.5486C>G
NM_001395677.1:c.5486C>G
NM_001395678.1:c.5486C>G
NM_001395679.1:c.5486C>G
NM_001395680.1:c.5486C>G
NM_001395682.1:c.5486C>G
NM_001395683.1:c.5486C>G
NM_001395684.1:c.5486C>G
NM_001395685.1:c.5486C>G
NM_001395686.1:c.5204C>G
NM_001395687.1:c.5081C>G
NM_001395688.1:c.5081C>G
NM_001395689.1:c.5081C>G
NM_001395690.1:c.5081C>G
NM_001395691.1:c.4919C>G
NM_001395697.1:c.3803C>G
NR_172715.1:n.5904C>G
NR_172716.1:n.6088C>G
NR_172717.1:n.5998C>G
NR_172718.1:n.5921C>G
NR_172719.1:n.5754C>G
NR_172720.1:n.5957C>G
More

Uncertain Significance

Met criteria codes 3
PM1_Supporting PM2_Supporting BP4
Not Met criteria codes 20
BA1 PS4 PS1 PS3 PS2 PVS1 PP4 PP1 PP3 PM6 PM3 PM5 PM4 BS3 BS4 BS1 BS2 BP5 BP7 BP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
DICER1 and miRNA-Processing Gene VCEP
The NM_177438.3:c.5486C>G variant in DICER1 is a missense variant predicted to cause substitution of threonine by arginine at amino acid 1829 (p.Thr1829Arg). Although this variant has been observed in individuals undergoing genetic sequencing, to our knowledge, this variant has not been reported in individuals with DICER1-related tumor predisposition (PS4 not met). This variant has an allele frequency of 0.000000619 (1/1614150 alleles) across gnomAD v4.1.0 with no more than one allele in any subpopulation, which is lower than the ClinGen DICER1 VCEP threshold (<0.000005) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). This variant resides within the RNase IIIb domain (PM1_Supporting; PMID: 31342592). The computational predictor REVEL gives a score of 0.347, which is below the threshold of 0.5, and the splice site predictors MaxEntScan and SpliceAI indicate that the variant has no impact on splicing, evidence that does not predict a damaging effect on DICER1 function (BP4). Due to conflicting evidence, this variant is classified as a variant of unknown significance for DICER1-related tumor predisposition based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: PM1_supporting, PM2_supporting, BP4. (Bayesian points 1; VCEP specifications version 1.4.0; 08/26/2025)
Met criteria codes
PM1_Supporting
This variant occurs in the RNase IIIb domain, which is a hotspot for missense variants associated with DICER1-related neoplasms (Heravi-Moussavi et al. 2012. PubMed ID: 22187960; Foulkes et al. 2014. PubMed ID: 25176334; Chen et al. 2018. PubMed ID: 31893257).
PM2_Supporting
This variant has an allele frequency of 0.000000619 (1/1614150 alleles) across gnomAD v4.1.0 with no more than one allele in any subpopulation, which is lower than the ClinGen DICER1 VCEP threshold (<0.000005) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
BP4
The computational predictor REVEL gives a score of 0.347, which is below the threshold of 0.5, and the splice site predictor SpliceAI indicates that the variant has no impact on splicing, evidence that does not predict a damaging effect on DICER1 function (BP4).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Although this variant has been observed in individuals undergoing genetic sequencing, to our knowledge, this variant has not been reported in individuals with DICER1-related tumor predisposition (PS4 not met; Internal lab contributors).
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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