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]
  • 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.4376G>A (p.Gly1459Glu)

CA265898350

543597 (ClinVar)

Gene: DICER1
Condition: DICER1-related tumor predisposition
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ceea5899-f471-4e54-aedc-9c91e19820a4
Approved on: 2024-04-23
Published on: 2024-05-08

HGVS expressions

NM_177438.3:c.4376G>A
NM_177438.3(DICER1):c.4376G>A (p.Gly1459Glu)
NC_000014.9:g.95096544C>T
CM000676.2:g.95096544C>T
NC_000014.8:g.95562881C>T
CM000676.1:g.95562881C>T
NC_000014.7:g.94632634C>T
NG_016311.1:g.65879G>A
ENST00000529720.2:c.4376G>A
ENST00000531162.7:c.4376G>A
ENST00000674628.2:c.4376G>A
ENST00000675540.2:c.*1026G>A
ENST00000696733.1:c.4376G>A
ENST00000696734.1:c.4376G>A
ENST00000696735.1:n.1363G>A
ENST00000696736.1:c.4376G>A
ENST00000696737.1:c.4376G>A
ENST00000696920.1:n.4639G>A
ENST00000696921.1:n.5482G>A
ENST00000696922.1:n.4785G>A
ENST00000696923.1:c.4376G>A
ENST00000696924.1:c.4376G>A
ENST00000696925.1:n.4785G>A
ENST00000343455.8:c.4376G>A
ENST00000393063.6:c.4376G>A
ENST00000526495.6:c.4376G>A
ENST00000532939.3:c.4376G>A
ENST00000556045.6:c.4376G>A
ENST00000675540.1:c.2121G>A
ENST00000675995.1:c.*2692G>A
ENST00000343455.7:c.4376G>A
ENST00000393063.5:c.4376G>A
ENST00000526495.5:c.4376G>A
ENST00000527414.5:c.4376G>A
ENST00000532939.2:c.411G>A
ENST00000541352.5:c.4376G>A
ENST00000556045.5:c.1070G>A
NM_001195573.1:c.4376G>A
NM_001271282.2:c.4376G>A
NM_001291628.1:c.4376G>A
NM_030621.4:c.4376G>A
NM_177438.2:c.4376G>A
NM_001271282.3:c.4376G>A
NM_001291628.2:c.4376G>A
NM_001395677.1:c.4376G>A
NM_001395678.1:c.4376G>A
NM_001395679.1:c.4376G>A
NM_001395680.1:c.4376G>A
NM_001395682.1:c.4376G>A
NM_001395683.1:c.4376G>A
NM_001395684.1:c.4376G>A
NM_001395685.1:c.4376G>A
NM_001395686.1:c.4094G>A
NM_001395687.1:c.3971G>A
NM_001395688.1:c.3971G>A
NM_001395689.1:c.3971G>A
NM_001395690.1:c.3971G>A
NM_001395691.1:c.3809G>A
NM_001395692.1:c.4376G>A
NM_001395693.1:c.4376G>A
NM_001395694.1:c.4376G>A
NM_001395695.1:c.4376G>A
NM_001395696.1:c.3971G>A
NM_001395697.1:c.2693G>A
NR_172715.1:n.4794G>A
NR_172716.1:n.4978G>A
NR_172717.1:n.4888G>A
NR_172718.1:n.4811G>A
NR_172719.1:n.4644G>A
NR_172720.1:n.4721G>A
More

Likely Benign

Met criteria codes 2
BS2_Supporting BP4
Not Met criteria codes 13
PS4 PS2 PS1 BA1 PP1 PP3 PM1 PM5 PM6 PM2 BS4 BS1 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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
DICER1 and miRNA-Processing Gene VCEP
The NM_177438.2:c.4376G>A variant in DICER1 is a missense variant predicted to cause substitution of glycine by glutamic acid at amino acid 1459 (p.Gly1459Glu). The total allele frequency in gnomAD v4.1.0 is 0.000004789 (7/1461620 alleles) with a highest population minor allele frequency of 0.00008955 (4/44670alleles) in the Admixed American population (PM2_Supporting, BS1, and BA1 are not met). This variant has been seen in 10 or more unrelated females without tumors through age 50 in at least one testing laboratory (BS2_Supporting; Internal lab contributors). In silico tools predict no damaging impact of the variant on protein function (REVEL: 0.476; SpliceAI and MaxEnt no effect on splicing) (BP4). 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: BS2_Supporting, BP4. (Bayesian Points: -2; VCEP specifications version 1.3.0; 04/23/2024)
Met criteria codes
BS2_Supporting
This variant has been seen in 10 or more unrelated females without tumors through age 50 in at least one testing laboratory (BS2_Supporting; Internal lab contributors). Invitae: 10 Ambry: 5 GeneDx: 1
BP4
In silico tools predict no damaging impact of the variant on protein function (REVEL: 0.476; SpliceAI and MaxEnt no effect on splicing) (BP4).
Not Met criteria codes
PS4
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
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
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
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 0.000004789 (7/1461620 alleles) with a highest population minor allele frequency of 0.00008955 (4/44670alleles) in the Admixed American population (PM2_Supporting, BS1, and BA1 are not met).
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
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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