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]

Variant: NM_177438.2(DICER1):c.1825G>T (p.Asp609Tyr)

CA158261

133965 (ClinVar)

Gene: DICER1
Condition: dicer1 syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ce2a208e-7e58-4c57-84aa-e9d89f32b6c7
Approved on: 2022-05-18
Published on: 2022-07-08

HGVS expressions

NM_177438.2:c.1825G>T
NM_177438.2(DICER1):c.1825G>T (p.Asp609Tyr)
NC_000014.9:g.95115749C>A
CM000676.2:g.95115749C>A
NC_000014.8:g.95582086C>A
CM000676.1:g.95582086C>A
NC_000014.7:g.94651839C>A
NG_016311.1:g.46674G>T
ENST00000343455.8:c.1825G>T
ENST00000393063.6:c.1825G>T
ENST00000526495.6:c.1825G>T
ENST00000532939.3:c.1825G>T
ENST00000556045.6:c.1825G>T
ENST00000675995.1:c.*141G>T
ENST00000343455.7:c.1825G>T
ENST00000393063.5:c.1825G>T
ENST00000526495.5:c.1825G>T
ENST00000527414.5:c.1825G>T
ENST00000532458.1:n.414G>T
ENST00000541352.5:c.1825G>T
NM_001195573.1:c.1825G>T
NM_001271282.2:c.1825G>T
NM_001291628.1:c.1825G>T
NM_030621.4:c.1825G>T
NM_001271282.3:c.1825G>T
NM_001291628.2:c.1825G>T
NM_177438.3:c.1825G>T
NM_001395677.1:c.1825G>T
NM_001395678.1:c.1825G>T
NM_001395679.1:c.1825G>T
NM_001395680.1:c.1825G>T
NM_001395682.1:c.1825G>T
NM_001395683.1:c.1825G>T
NM_001395684.1:c.1825G>T
NM_001395685.1:c.1825G>T
NM_001395686.1:c.1543G>T
NM_001395687.1:c.1420G>T
NM_001395688.1:c.1420G>T
NM_001395689.1:c.1420G>T
NM_001395690.1:c.1420G>T
NM_001395691.1:c.1258G>T
NM_001395692.1:c.1825G>T
NM_001395693.1:c.1825G>T
NM_001395694.1:c.1825G>T
NM_001395695.1:c.1825G>T
NM_001395696.1:c.1420G>T
NM_001395697.1:c.142G>T
NM_001395698.1:c.1420G>T
NR_172715.1:n.2243G>T
NR_172716.1:n.2170G>T
NR_172717.1:n.2337G>T
NR_172718.1:n.2337G>T
NR_172719.1:n.2170G>T
NR_172720.1:n.2170G>T
NM_177438.3(DICER1):c.1825G>T (p.Asp609Tyr)
More

Benign

Met criteria codes 3
BA1 BS2 BP4
Not Met criteria codes 15
PS2 PS4 PS3 PS1 PP4 PP1 PP3 PM6 PM2 PM1 PM5 BS4 BS3 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

PDF
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.1825G>T variant in DICER1 is a missense variant predicted to cause substitution of Aspartic Acid by Tyrosine at amino acid 609 (p.Asp609Tyr). The highest population minor allele frequency in gnomAD non cancer dataset v2.1.1 is 0.006310 (149/23614 alleles) in the African population, which is higher than the ClinGen DICER1 VCEP threshold (>0.003) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for DICER1 syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: BA1. (Bayesian Points: NA; VCEP specifications version 1; 02/11/2022)
Met criteria codes
BA1
AF of 0.006488 in African subpop with 168 alleles.
BS2
This variant has been seen in 40 or more unrelated females without tumors through age 50 in at least one testing laboratory (SCV000291623.7, SCV000661837.3) and has been observed in a homozygous state in 3 healthy individuals and/or individuals without clinical data (SCV000291623.7)
BP4
REVEL score 0.2. No splicing effects.
Not Met criteria codes
PS2
No accurate de novo cases reported
PS4
No individuals reported with DICER1 phenotype. Rule also cannot be applied as variants meets BA1/BS1.
PS3
No relevant functional assays found
PS1
Only variant found in this codon in ClinVar
PP4
No reported phenotype/fam hx to meet
PP1
No phenotype-positive families reported
PP3
REVEL score 0.2
PM6
No accurate de novo cases reported
PM2
Present in gnomAD
PM1
Not in a mutational hostpot or established functional domain
PM5
Only variant found in this codon in ClinVar
BS4
No phenotype-positive families reported
BS3
No relevant functional assays found
BS1
AF of 0.006488 in African subpop with 168 alleles.
BP2
Not observed
Curation History
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