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.4423A>G (p.Thr1475Ala)

CA7330848

477204 (ClinVar)

Gene: DICER1
Condition: DICER1-related tumor predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 35ec7ef0-e59b-4125-80d1-846de74b6ed5
Approved on: 2024-02-27
Published on: 2024-05-08

HGVS expressions

NM_177438.3:c.4423A>G
NM_177438.3(DICER1):c.4423A>G (p.Thr1475Ala)
NC_000014.9:g.95096497T>C
CM000676.2:g.95096497T>C
NC_000014.8:g.95562834T>C
CM000676.1:g.95562834T>C
NC_000014.7:g.94632587T>C
NG_016311.1:g.65926A>G
ENST00000529720.2:c.4423A>G
ENST00000531162.7:c.4423A>G
ENST00000674628.2:c.4423A>G
ENST00000675540.2:c.*1073A>G
ENST00000696733.1:c.4423A>G
ENST00000696734.1:c.4423A>G
ENST00000696735.1:n.1410A>G
ENST00000696736.1:c.4423A>G
ENST00000696737.1:c.4423A>G
ENST00000696920.1:n.4686A>G
ENST00000696921.1:n.5529A>G
ENST00000696922.1:n.4832A>G
ENST00000696923.1:c.4423A>G
ENST00000696924.1:c.4423A>G
ENST00000696925.1:n.4832A>G
ENST00000343455.8:c.4423A>G
ENST00000393063.6:c.4423A>G
ENST00000526495.6:c.4423A>G
ENST00000532939.3:c.4423A>G
ENST00000556045.6:c.4423A>G
ENST00000675540.1:c.2168A>G
ENST00000675995.1:c.*2739A>G
ENST00000343455.7:c.4423A>G
ENST00000393063.5:c.4423A>G
ENST00000526495.5:c.4423A>G
ENST00000527414.5:c.4423A>G
ENST00000532939.2:c.458A>G
ENST00000541352.5:c.4423A>G
ENST00000556045.5:c.1117A>G
NM_001195573.1:c.4423A>G
NM_001271282.2:c.4423A>G
NM_001291628.1:c.4423A>G
NM_030621.4:c.4423A>G
NM_177438.2:c.4423A>G
NM_001271282.3:c.4423A>G
NM_001291628.2:c.4423A>G
NM_001395677.1:c.4423A>G
NM_001395678.1:c.4423A>G
NM_001395679.1:c.4423A>G
NM_001395680.1:c.4423A>G
NM_001395682.1:c.4423A>G
NM_001395683.1:c.4423A>G
NM_001395684.1:c.4423A>G
NM_001395685.1:c.4423A>G
NM_001395686.1:c.4141A>G
NM_001395687.1:c.4018A>G
NM_001395688.1:c.4018A>G
NM_001395689.1:c.4018A>G
NM_001395690.1:c.4018A>G
NM_001395691.1:c.3856A>G
NM_001395692.1:c.4423A>G
NM_001395693.1:c.4423A>G
NM_001395694.1:c.4423A>G
NM_001395695.1:c.4423A>G
NM_001395696.1:c.4018A>G
NM_001395697.1:c.2740A>G
NR_172715.1:n.4841A>G
NR_172716.1:n.5025A>G
NR_172717.1:n.4935A>G
NR_172718.1:n.4858A>G
NR_172719.1:n.4691A>G
NR_172720.1:n.4768A>G
More

Uncertain Significance

Met criteria codes 2
BS2_Supporting BP4
Not Met criteria codes 24
PM6 PM2 PM3 PM1 PM4 PM5 PVS1 BA1 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP1 PS4 PS2 PS3 PS1 PP1 PP4 PP3 PP2

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.4423A>G variant in DICER1 is a missense variant predicted to cause substitution of threonine by alanine at amino acid 1475 (p.Thr1475Ala). This variant was observed in a proband with medulloepithelioma, type unspecified (PS4 not met; Internal lab contributor). 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). The highest population minor allele frequency in gnomAD v4.1.0 is 0.0003287 (2/6084 alleles) in the Middle Eastern population (PM2_Supporting, BS1, and BA1 are not met). In silico tools predict no damaging impact of the variant on protein function (REVEL: 0.058; MaxEntScan and SpliceAI: no effect on splicing) (BP4). Though this variant meets the criteria to be classified as Likely Benign for DICER1-related tumor predisposition based on the ACMG/AMP criteria applied (BS2_Supporting, BP4), the ClinGen DICER1 VCEP has decided to override classification to Uncertain Significance due to the potential observation of ciliary body medulloepithelioma (a high-specificity phenotype) in a proband with limited available clinical data. (Bayesian Points: -2; VCEP specifications version 1.3.0; 02/27/2024)
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; GTR IDs: 61756, 500031).
BP4
In silico tools predict no damaging impact of the variant on protein function (REVEL: 0.058; MaxEntScan and SpliceAI: no effect on splicing) (BP4).
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The highest population minor allele frequency in gnomAD v4.1.0 is 0.0003287 (2/6084 alleles) in the Middle Eastern population (PM2_Supporting, BS1, and BA1 are not met).
PM3
This evidence code is not currently applicable for DICER1 VCEP curations.
PM1
This variant does not reside within a region of the RNAse IIIb domain that is defined as a mutational hotspot or critical functional domain by the ClinGen DICER1 VCEP (PM1 not met).
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
2 different missense variants, c.4424C>T (p.Thr1475Ile) and c.4423A>C (p.Thr1475Pro) [ClinVar SCV IDs: SCV002628273.1, SCV002163741.2, SCV002589399.2] in the same codon have been classified as Uncertain Significance for DICER1-related tumor predisposition in ClinVar.
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 v4.1.0 is 0.0003287 (2/6084 alleles) in the Middle Eastern 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
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 v4.1.0 is 0.0003287 (2/6084 alleles) in the Middle Eastern population (PM2_Supporting, BS1, and BA1 are not met).
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
This evidence code is not currently applicable for DICER1 VCEP curations.
PS4
This variant was observed in a proband with medulloepithelioma, type unspecified (PS4 not met; GTR ID: 500031).
PS2
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
PS1
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
In silico tools predict no damaging impact of the variant on protein function (REVEL: 0.058; MaxEntScan and SpliceAI: no effect on splicing) (BP4).
PP2
This evidence code is not currently applicable for DICER1 VCEP curations.
Curation History
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