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]
Link to SEPIO compliant JSON-LD document

Variant: NM_177438.2(DICER1):c.4647C>T (p.His1549=)

CA7330821

417113 (ClinVar)

Gene: DICER1
Condition: dicer1 syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9a08eb3a-ea3b-41fa-8f25-915b5bbcdb0a
Approved on: 2022-05-18
Published on: 2022-07-08

HGVS expressions

NM_177438.2:c.4647C>T
NM_177438.2(DICER1):c.4647C>T (p.His1549=)
NC_000014.9:g.95096273G>A
CM000676.2:g.95096273G>A
NC_000014.8:g.95562610G>A
CM000676.1:g.95562610G>A
NC_000014.7:g.94632363G>A
NG_016311.1:g.66150C>T
ENST00000343455.8:c.4647C>T
ENST00000393063.6:c.4647C>T
ENST00000526495.6:c.4647C>T
ENST00000532939.3:c.4647C>T
ENST00000556045.6:c.4647C>T
ENST00000675540.1:n.2392C>T
ENST00000675995.1:c.*2963C>T
ENST00000343455.7:c.4647C>T
ENST00000393063.5:c.4647C>T
ENST00000526495.5:c.4647C>T
ENST00000527414.5:c.4647C>T
ENST00000532939.2:n.682C>T
ENST00000541352.5:c.4647C>T
ENST00000556045.5:c.1341C>T
NM_001195573.1:c.4647C>T
NM_001271282.2:c.4647C>T
NM_001291628.1:c.4647C>T
NM_030621.4:c.4647C>T
NM_001271282.3:c.4647C>T
NM_001291628.2:c.4647C>T
NM_177438.3:c.4647C>T
NM_001395677.1:c.4647C>T
NM_001395678.1:c.4647C>T
NM_001395679.1:c.4647C>T
NM_001395680.1:c.4647C>T
NM_001395682.1:c.4647C>T
NM_001395683.1:c.4647C>T
NM_001395684.1:c.4647C>T
NM_001395685.1:c.4647C>T
NM_001395686.1:c.4365C>T
NM_001395687.1:c.4242C>T
NM_001395688.1:c.4242C>T
NM_001395689.1:c.4242C>T
NM_001395690.1:c.4242C>T
NM_001395691.1:c.4080C>T
NM_001395692.1:c.4647C>T
NM_001395693.1:c.4647C>T
NM_001395694.1:c.4647C>T
NM_001395695.1:c.4647C>T
NM_001395696.1:c.4242C>T
NM_001395697.1:c.2964C>T
NR_172715.1:n.5065C>T
NR_172716.1:n.5249C>T
NR_172717.1:n.5159C>T
NR_172718.1:n.5082C>T
NR_172719.1:n.4915C>T
NR_172720.1:n.4992C>T
NM_177438.3(DICER1):c.4647C>T (p.His1549=)

Likely Benign

Met criteria codes 3
BS2 BP4 BP7
Not Met criteria codes 16
PP4 PP1 PP3 BS4 BS3 BS1 BP2 PS2 PS4 PS3 PS1 BA1 PM1 PM5 PM6 PM2

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.4647C>T (p.His1549=) variant is a synonymous (silent) variant that is not predicted by MaxEntScan or SpliceAI to impact splicing (BP4, BP7). This variant has been seen in 40 or more unrelated females without tumors through age 50 in at least one testing laboratory (SCV000661822.3, SCV000563438.6) (BS2). 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: BP7, BP4, BS2. (Bayesian Points: -6; VCEP specifications version 1; 02/11/2022)
Met criteria codes
BS2
This variant has been seen in 40 or more unrelated females without tumors through age 50 in at least one testing laboratory (SCV000661822.3, SCV000563438.6).
BP4
VarSEAK, MES, and SpliceAI concordance of no predicted splicing impact.
BP7
UCSC Genome Browser (14: 95562610 (GRCh37); Variant allele seen in 3+ mammals: armadillo, opossum, tasmainian devil, wallaby, and platypus . Splicing not impacted
Not Met criteria codes
PP4
No applicable cases in literature or internal data
PP1
No family data reported
PP3
No REVEL score
BS4
No family data reported
BS3
No splicing impact, but no RNA studies found
BS1
Freq cutoff not met
BP2
No reports found
PS2
No cases in internal data or literature
PS4
No individuals with phenotype in internal data or literature
PS3
No data found
PS1
No other variants in ClinVar
BA1
Freq cutoff not met
PM1
Not in hotspot region
PM5
No other variants in ClinVar
PM6
No cases in internal data or literature
PM2
Present in gnomAD
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