rs763704682
Positions:
- chr14-95099771-C-CACAA
- chr14-95099771-C-CACAAAA
- chr14-95099771-C-CACACAA
- chr14-95099771-C-CACACAAAA
- chr14-95099771-C-CACACACAA
- chr14-95099771-C-CACACACAAAA
- chr14-95099771-C-CACACACACAA
- chr14-95099771-C-CACACACACACAA
- chr14-95099771-C-CACACACACACACAA
- chr14-95099771-C-CACACACACACACACAA
- chr14-95099771-C-CACACACACACACACACAA
- chr14-95099771-C-CACACACACACACACACACACACAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_177438.3(DICER1):c.4206+8_4206+9insTTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 26,826 control chromosomes in the GnomAD database, including 52 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.053 ( 52 hom., cov: 30)
Exomes 𝑓: 0.0045 ( 44 hom. )
Failed GnomAD Quality Control
Consequence
DICER1
NM_177438.3 intron
NM_177438.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.425
Genes affected
DICER1 (HGNC:17098): (dicer 1, ribonuclease III) This gene encodes a protein possessing an RNA helicase motif containing a DEXH box in its amino terminus and an RNA motif in the carboxy terminus. The encoded protein functions as a ribonuclease and is required by the RNA interference and small temporal RNA (stRNA) pathways to produce the active small RNA component that represses gene expression. This protein also acts as a strong antiviral agent with activity against RNA viruses, including the Zika and SARS-CoV-2 viruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 14-95099771-C-CACAA is Benign according to our data. Variant chr14-95099771-C-CACAA is described in ClinVar as [Benign]. Clinvar id is 221051.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DICER1 | NM_177438.3 | c.4206+8_4206+9insTTGT | intron_variant | ENST00000343455.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DICER1 | ENST00000343455.8 | c.4206+8_4206+9insTTGT | intron_variant | 1 | NM_177438.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0528 AC: 1413AN: 26746Hom.: 54 Cov.: 30
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GnomAD3 exomes AF: 0.00329 AC: 561AN: 170614Hom.: 183 AF XY: 0.00241 AC XY: 223AN XY: 92356
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00449 AC: 1231AN: 274410Hom.: 44 Cov.: 34 AF XY: 0.00432 AC XY: 581AN XY: 134510
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.0528 AC: 1416AN: 26826Hom.: 52 Cov.: 30 AF XY: 0.0491 AC XY: 640AN XY: 13032
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
DICER1-related tumor predisposition Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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Name
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at