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

Variant: NM_177438.3(DICER1):c.1089C>T (p.Phe363=)

CA10583223

242030 (ClinVar)

Gene: DICER1
Condition: DICER1-related tumor predisposition
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: c13d3d4a-1321-4983-b5b8-da45714e3656
Approved on: 2024-04-23
Published on: 2024-05-08

HGVS expressions

NM_177438.3:c.1089C>T
NM_177438.3(DICER1):c.1089C>T (p.Phe363=)
NC_000014.9:g.95124483G>A
CM000676.2:g.95124483G>A
NC_000014.8:g.95590820G>A
CM000676.1:g.95590820G>A
NC_000014.7:g.94660573G>A
NG_016311.1:g.37940C>T
ENST00000529720.2:c.1089C>T
ENST00000531162.7:c.1089C>T
ENST00000674628.2:c.1089C>T
ENST00000675540.2:c.1089C>T
ENST00000696733.1:c.1089C>T
ENST00000696734.1:c.1089C>T
ENST00000696736.1:c.1089C>T
ENST00000696737.1:c.1089C>T
ENST00000696921.1:n.2195C>T
ENST00000696922.1:n.1498C>T
ENST00000696923.1:c.1089C>T
ENST00000696924.1:c.1089C>T
ENST00000696925.1:n.1498C>T
ENST00000696927.1:n.692C>T
ENST00000696928.1:n.1286C>T
ENST00000343455.8:c.1089C>T
ENST00000393063.6:c.1089C>T
ENST00000526495.6:c.1089C>T
ENST00000532939.3:c.1089C>T
ENST00000556045.6:c.1089C>T
ENST00000674628.1:c.1089C>T
ENST00000675995.1:c.1089C>T
ENST00000343455.7:c.1089C>T
ENST00000393063.5:c.1089C>T
ENST00000526495.5:c.1089C>T
ENST00000527414.5:c.1089C>T
ENST00000541352.5:c.1089C>T
NM_001195573.1:c.1089C>T
NM_001271282.2:c.1089C>T
NM_001291628.1:c.1089C>T
NM_030621.4:c.1089C>T
NM_177438.2:c.1089C>T
NM_001271282.3:c.1089C>T
NM_001291628.2:c.1089C>T
NM_001395677.1:c.1089C>T
NM_001395678.1:c.1089C>T
NM_001395679.1:c.1089C>T
NM_001395680.1:c.1089C>T
NM_001395682.1:c.1089C>T
NM_001395683.1:c.1089C>T
NM_001395684.1:c.1089C>T
NM_001395685.1:c.1089C>T
NM_001395686.1:c.807C>T
NM_001395687.1:c.684C>T
NM_001395688.1:c.684C>T
NM_001395689.1:c.684C>T
NM_001395690.1:c.684C>T
NM_001395691.1:c.522C>T
NM_001395692.1:c.1089C>T
NM_001395693.1:c.1089C>T
NM_001395694.1:c.1089C>T
NM_001395695.1:c.1089C>T
NM_001395696.1:c.684C>T
NM_001395697.1:c.-480C>T
NM_001395698.1:c.684C>T
NM_001395699.1:c.1089C>T
NM_001395700.1:c.1089C>T
NR_172715.1:n.1303C>T
NR_172716.1:n.1434C>T
NR_172717.1:n.1601C>T
NR_172718.1:n.1601C>T
NR_172719.1:n.1434C>T
NR_172720.1:n.1434C>T

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 11
BS4 BS1 PS2 PS1 BP2 PP1 BA1 PM6 PM2 PM1 PM5

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 1.3.0

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.1089C>T (p.Phe363=) variant is a synonymous (silent) variant that is not predicted to impact splicing by MaxEntScan or SpliceAI (BP4, BP7). The total allele frequency in gnomAD v4.1.0 is 0.000001368 (2/1461842 alleles) with a highest population minor allele frequency of 0.00003312 (2/60394 alleles) in a population of undisclosed ancestry (PM2_Supporting, BS1, and BA1 are not met). In summary, this variant meets the criteria to be classified as Likely Benign for DICER1-related tumor predisposition based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: BP4, BP7. (Bayesian Points: -2; VCEP specifications version 1.3.0; 04/23/2024)
Met criteria codes
BP7
The NM_177438.3:c.1089C>T (p.Phe363=) variant is a synonymous (silent) variant that is not predicted to impact splicing by MaxEntScan or SpliceAI (BP4, BP7).
BP4
The NM_177438.3:c.1089C>T (p.Phe363=) variant is a synonymous (silent) variant that is not predicted to impact splicing by MaxEntScan or SpliceAI (BP4, BP7).
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The total allele frequency in gnomAD v4.1.0 is 0.000001368 (2/1461842 alleles) with a highest population minor allele frequency of 0.00003312 (2/60394 alleles) in a population of undisclosed ancestry (PM2_Supporting, BS1, and BA1 are not met).
PS2
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
BP2
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
BA1
The total allele frequency in gnomAD v4.1.0 is 0.000001368 (2/1461842 alleles) with a highest population minor allele frequency of 0.00003312 (2/60394 alleles) in a population of undisclosed ancestry (PM2_Supporting, BS1, and BA1 are not met).
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The total allele frequency in gnomAD v4.1.0 is 0.000001368 (2/1461842 alleles) with a highest population minor allele frequency of 0.00003312 (2/60394 alleles) in a population of undisclosed ancestry (PM2_Supporting, BS1, and BA1 are not met).
PM1
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
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