The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_177438.3(DICER1):c.5461A>G (p.Met1821Val)

CA16614591

412149 (ClinVar)

Gene: DICER1
Condition: DICER1-related tumor predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 6ec0d621-923b-406d-90b2-f1375482dc69
Approved on: 2023-07-10
Published on: 2023-07-20

HGVS expressions

NM_177438.3:c.5461A>G
NM_177438.3(DICER1):c.5461A>G (p.Met1821Val)
NC_000014.9:g.95091269T>C
CM000676.2:g.95091269T>C
NC_000014.8:g.95557606T>C
CM000676.1:g.95557606T>C
NC_000014.7:g.94627359T>C
NG_016311.1:g.71154A>G
ENST00000343455.8:c.5461A>G
ENST00000393063.6:c.5461A>G
ENST00000526495.6:c.5461A>G
ENST00000556045.6:c.*178A>G
ENST00000675540.1:n.3206A>G
ENST00000675995.1:c.*3777A>G
ENST00000343455.7:c.5461A>G
ENST00000393063.5:c.5461A>G
ENST00000526495.5:c.5461A>G
ENST00000527414.5:c.5461A>G
ENST00000527416.2:n.54A>G
ENST00000527554.2:n.154A>G
ENST00000541352.5:c.5365-160A>G
ENST00000556045.5:c.2155A>G
NM_001195573.1:c.5365-160A>G
NM_001271282.2:c.5461A>G
NM_001291628.1:c.5461A>G
NM_030621.4:c.5461A>G
NM_177438.2:c.5461A>G
NM_001271282.3:c.5461A>G
NM_001291628.2:c.5461A>G
NM_001395677.1:c.5461A>G
NM_001395678.1:c.5461A>G
NM_001395679.1:c.5461A>G
NM_001395680.1:c.5461A>G
NM_001395682.1:c.5461A>G
NM_001395683.1:c.5461A>G
NM_001395684.1:c.5461A>G
NM_001395685.1:c.5461A>G
NM_001395686.1:c.5179A>G
NM_001395687.1:c.5056A>G
NM_001395688.1:c.5056A>G
NM_001395689.1:c.5056A>G
NM_001395690.1:c.5056A>G
NM_001395691.1:c.4894A>G
NM_001395697.1:c.3778A>G
NR_172715.1:n.5879A>G
NR_172716.1:n.6063A>G
NR_172717.1:n.5973A>G
NR_172718.1:n.5896A>G
NR_172719.1:n.5729A>G
NR_172720.1:n.5932A>G
More

Uncertain Significance

Met criteria codes 2
PM1_Supporting PM2_Supporting
Not Met criteria codes 24
BP5 BP7 BP2 BP3 BP4 BP1 PS4 PS3 PS1 PS2 PP4 PP1 PP3 PP2 PM3 PM5 PM4 PM6 PVS1 BA1 BS4 BS3 BS1 BS2

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
DICER1 and miRNA-Processing Gene VCEP
The NM_177438.2:c.5461A>G variant in DICER1 is a missense variant predicted to cause substitution of methionine by valine at amino acid 1821 (p.Met1821Val). This variant has an allele frequency of 0.000004 (1/236,934 alleles) across gnomAD v2.1.1 (non-cancer) 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). The computational predictor REVEL gives a score of 0.54, which is neither above nor below the thresholds predicting a damaging or benign impact on DICER1 function (PP3 and BP4 not met). This variant resides within the RNase IIIb domain of DICER1, a mutational hotspot domain with critical functionality as defined by the ClinGen DICER1 VCEP (PM1_Supporting; PMID: 31342592). In summary, this variant meets the criteria to be classified as Uncertain Significance for DICER1-related tumor predisposition based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: PM1_Supporting, PM2_Supporting. (Bayesian Points: 2; VCEP specifications version 1.2.0; 07/10/2023)
Met criteria codes
PM1_Supporting
This variant resides within the RNase IIIb domain of DICER1, a mutational hotspot domain with critical functionality as defined by the ClinGen DICER1 VCEP (PM1_Supporting; PMID: 31342592).
PM2_Supporting
This variant has an allele frequency of 0.000004 (1/236,934 alleles) across gnomAD v2.1.1 (non-cancer) 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).
Not Met criteria codes
BP5
This evidence code is not currently applicable for DICER1 VCEP curations.
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
BP3
This evidence code is not currently applicable for DICER1 VCEP curations.
BP4
The computational predictor REVEL gives a score of 0.54, which is neither above nor below the thresholds predicting a damaging or benign impact on DICER1 function (PP3 and BP4 not met).
BP1
This evidence code is not currently applicable for DICER1 VCEP curations.
PS4
This variant received a total of 0 phenotype points across 7 unrelated probands (Invitae internal data) and 0 phenotype points across 10 unrelated probands. (PS4 not met; Ambry internal data).
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
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
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
The computational predictor REVEL gives a score of 0.54, which is neither above nor below the thresholds predicting a damaging or benign impact on DICER1 function (PP3 and BP4 not met).
PP2
This evidence code is not currently applicable for DICER1 VCEP curations.
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Another missense variants, c.5461A>C (p.Met1821Leu), in the same codon has not been classified as pathogenic for DICER1 syndrome by the ClinGen DICER1 VCEP.
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
This evidence code is not currently applicable for DICER1 VCEP curations.
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/34,260 alleles) in the Latino population, which is less than the ClinGen DICER1 VCEP threshold (>0.003) for BA1 (BA1 not met).
BS4
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
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/34,260 alleles) in the Latino population, which is less than the ClinGen DICER1 VCEP threshold (>0.0003) for BS1 (BS1 not met).
BS2
This variant has been seen in 2 unrelated females (Invitae internal data) and 5 unrelated females (Ambry internal data) without tumors through age 50.
Curation History
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