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.5052C>G (p.Leu1684=)

CA7330753

242128 (ClinVar)

Gene: DICER1
Condition: dicer1 syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: fad42e66-5505-4cb8-a663-ef3d633e0ad8
Approved on: 2022-05-18
Published on: 2022-07-08

HGVS expressions

NM_177438.2:c.5052C>G
NM_177438.2(DICER1):c.5052C>G (p.Leu1684=)
NC_000014.9:g.95095868G>C
CM000676.2:g.95095868G>C
NC_000014.8:g.95562205G>C
CM000676.1:g.95562205G>C
NC_000014.7:g.94631958G>C
NG_016311.1:g.66555C>G
ENST00000343455.8:c.5052C>G
ENST00000393063.6:c.5052C>G
ENST00000526495.6:c.5052C>G
ENST00000532939.3:c.5052C>G
ENST00000556045.6:c.5052C>G
ENST00000675540.1:n.2797C>G
ENST00000675995.1:c.*3368C>G
ENST00000343455.7:c.5052C>G
ENST00000393063.5:c.5052C>G
ENST00000526495.5:c.5052C>G
ENST00000527414.5:c.5052C>G
ENST00000532939.2:n.1087C>G
ENST00000541352.5:c.5052C>G
ENST00000556045.5:c.1746C>G
NM_001195573.1:c.5052C>G
NM_001271282.2:c.5052C>G
NM_001291628.1:c.5052C>G
NM_030621.4:c.5052C>G
NM_001271282.3:c.5052C>G
NM_001291628.2:c.5052C>G
NM_177438.3:c.5052C>G
NM_001395677.1:c.5052C>G
NM_001395678.1:c.5052C>G
NM_001395679.1:c.5052C>G
NM_001395680.1:c.5052C>G
NM_001395682.1:c.5052C>G
NM_001395683.1:c.5052C>G
NM_001395684.1:c.5052C>G
NM_001395685.1:c.5052C>G
NM_001395686.1:c.4770C>G
NM_001395687.1:c.4647C>G
NM_001395688.1:c.4647C>G
NM_001395689.1:c.4647C>G
NM_001395690.1:c.4647C>G
NM_001395691.1:c.4485C>G
NM_001395692.1:c.5052C>G
NM_001395693.1:c.5052C>G
NM_001395694.1:c.5052C>G
NM_001395695.1:c.5052C>G
NM_001395696.1:c.4647C>G
NM_001395697.1:c.3369C>G
NR_172715.1:n.5470C>G
NR_172716.1:n.5654C>G
NR_172717.1:n.5564C>G
NR_172718.1:n.5487C>G
NR_172719.1:n.5320C>G
NR_172720.1:n.5397C>G
NM_177438.3(DICER1):c.5052C>G (p.Leu1684=)
More

Likely Benign

Met criteria codes 3
BS1 BP7 BP4
Not Met criteria codes 11
PM6 PM2 PM1 BA1 BS4 BS3 PS2 PS3 PP3 PP4 PP1

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.5052C>G (p.Leu1684=) variant is a synonymous (silent) variant that is not predicted by MaxEntScan or SpliceAI to impact splicing (BP4, BP7). The highest population minor allele frequency in gnomAD v2.1.1 non-cancer is 0.0034 (5/14900 alleles) in African/African-American population, which is higher than the ClinGen DICER1 VCEP threshold (>0.0003) for BS1, and therefore meets this criterion (BS1). In summary, this variant meets the criteria to be classified as likely benign for DICER1 syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: BP4, BP7, BS1 (Bayesian Points: -6; VCEP specifications version 1; 02/11/22).
Met criteria codes
BS1
African subpop 0.034% AF (5/14900) in gnomAD 2.1 (non-cancer)
BP7
variant is a synonymous (silent) variant that is not predicted by MaxEntScan or SpliceAI to impact splicing (BP4, BP7).
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
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
PP3
No splicing impact predicted
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
Curation History
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