chr14-95094107-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_177438.3(DICER1):c.5145C>T(p.Leu1715Leu) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,614,130 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_177438.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 184AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 343AN: 251202Hom.: 1 AF XY: 0.00131 AC XY: 178AN XY: 135794
GnomAD4 exome AF: 0.00172 AC: 2516AN: 1461890Hom.: 3 Cov.: 33 AF XY: 0.00165 AC XY: 1202AN XY: 727244
GnomAD4 genome AF: 0.00121 AC: 184AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.00129 AC XY: 96AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:7
This variant is associated with the following publications: (PMID: 23547758, 21266384) -
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DICER1: BP4, BS1 -
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not specified Benign:4
ACMG criteria met: BS2, BP4, BP6, BP7 -
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DICER1-related tumor predisposition Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Hereditary cancer-predisposing syndrome Benign:2
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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Pleuropulmonary blastoma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at