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]
  • No ClinVar Id was directly found from the curated document

Variant: NR_172720.1:n.2995+5_2995+7del

CA2573320295

Gene: DICER1
Condition: dicer1 syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9aebc673-f29a-4be9-911f-e7ab2b26e1c2
Approved on: 2023-02-03
Published on: 2023-02-03

HGVS expressions

NR_172720.1:n.2995+5_2995+7del
NC_000014.9:g.95107875_95107877del
CM000676.2:g.95107875_95107877del
NC_000014.8:g.95574212_95574214del
CM000676.1:g.95574212_95574214del
NC_000014.7:g.94643965_94643967del
NG_016311.1:g.54548_54550del
ENST00000343455.8:c.2650+5_2650+7del
ENST00000393063.6:c.2650+5_2650+7del
ENST00000526495.6:c.2650+5_2650+7del
ENST00000532939.3:c.2650+5_2650+7del
ENST00000556045.6:c.2650+5_2650+7del
ENST00000675540.1:n.472+5_472+7del
ENST00000675995.1:c.*966+5_*966+7del
ENST00000343455.7:c.2650+5_2650+7del
ENST00000393063.5:c.2650+5_2650+7del
ENST00000526495.5:c.2650+5_2650+7del
ENST00000527414.5:c.2650+5_2650+7del
ENST00000541352.5:c.2650+5_2650+7del
NM_001195573.1:c.2650+5_2650+7del
NM_001271282.2:c.2650+5_2650+7del
NM_001291628.1:c.2650+5_2650+7del
NM_030621.4:c.2650+5_2650+7del
NM_177438.2:c.2650+5_2650+7del
NM_001271282.3:c.2650+5_2650+7del
NM_001291628.2:c.2650+5_2650+7del
NM_177438.3:c.2650+5_2650+7del
NM_001395677.1:c.2650+5_2650+7del
NM_001395678.1:c.2650+5_2650+7del
NM_001395679.1:c.2650+5_2650+7del
NM_001395680.1:c.2650+5_2650+7del
NM_001395682.1:c.2650+5_2650+7del
NM_001395683.1:c.2650+5_2650+7del
NM_001395684.1:c.2650+5_2650+7del
NM_001395685.1:c.2650+5_2650+7del
NM_001395686.1:c.2368+5_2368+7del
NM_001395687.1:c.2245+5_2245+7del
NM_001395688.1:c.2245+5_2245+7del
NM_001395689.1:c.2245+5_2245+7del
NM_001395690.1:c.2245+5_2245+7del
NM_001395691.1:c.2083+5_2083+7del
NM_001395692.1:c.2650+5_2650+7del
NM_001395693.1:c.2650+5_2650+7del
NM_001395694.1:c.2650+5_2650+7del
NM_001395695.1:c.2650+5_2650+7del
NM_001395696.1:c.2245+5_2245+7del
NM_001395697.1:c.967+5_967+7del
NR_172715.1:n.3068+5_3068+7del
NR_172716.1:n.2995+5_2995+7del
NR_172717.1:n.3162+5_3162+7del
NR_172718.1:n.3162+5_3162+7del
NR_172719.1:n.2995+5_2995+7del
More

Uncertain Significance

Met criteria codes 3
PP3 PM2_Supporting PS4_Supporting
Not Met criteria codes 18
PS3 PS2 PS1 PP4 PP1 BA1 PM6 PM4 PM1 PM5 BS2 BS3 BS4 BS1 BP7 BP2 BP4 PVS1

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

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.2650+5_2650+7delGAA variant in DICER1 is an intronic variant in intron 15. This variant received a total of 1 phenotype point across 1 unrelated proband/family meeting DICER1 VCEP phenotype specificity scoring criteria of 1-1.5 points (PS4_Supporting; Internal lab data: GTR500031). This variant is absent from gnomAD v2.1.1 and v3.1.2 (non-cancer) (PM2_Supporting). The splice site predictors MaxEntScan and SpliceAI indicate that the variant impacts splicing, evidence that correlates with impact to DICER1 function (PP3). In summary, this variant meets the criteria to be classified as uncertain significance for DICER1 syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: PS4_Supporting, PM2_supporting, PP3 (Bayesian Points: 3; VCEP specifications version 1.1.0; 01/23/2023).
Met criteria codes
PP3
Both SpliceAI and MaxEntScan predict splicing impact
PM2_Supporting
Absent in gnomAD v2.1.1 and v3.1.2 (non-cancer) with good coverage
PS4_Supporting
This variant received a total of 1 phenotype point across 1 unrelated proband/family meeting DICER1 VCEP phenotype specificity scoring criteria of 1-1.5 points
Not Met criteria codes
PS3
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
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
BA1
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
PM4
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
BS2
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
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
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
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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