chr14-95099771-C-CACACACACACACAA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_177438.3(DICER1):c.4206+8_4206+9insTTGTGTGTGTGTGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000522 in 26,844 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000025 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DICER1
NM_177438.3 splice_region, intron
NM_177438.3 splice_region, 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 -10 ACMG points.
BP6
Variant 14-95099771-C-CACACACACACACAA is Benign according to our data. Variant chr14-95099771-C-CACACACACACACAA is described in ClinVar as [Likely_benign]. Clinvar id is 477184.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000522 (14/26844) while in subpopulation AFR AF= 0.00094 (13/13836). AF 95% confidence interval is 0.000556. There are 0 homozygotes in gnomad4. There are 9 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000523 AC: 14AN: 26764Hom.: 0 Cov.: 30
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000255 AC: 7AN: 274866Hom.: 0 Cov.: 34 AF XY: 0.0000223 AC XY: 3AN XY: 134704
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.000522 AC: 14AN: 26844Hom.: 0 Cov.: 30 AF XY: 0.000690 AC XY: 9AN XY: 13040
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DICER1-related tumor predisposition Benign:1
Jan 28, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at