chr14-95099771-C-CACACAA

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_177438.3(DICER1):​c.4206+8_4206+9insTTGTGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 26,840 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 10 hom., cov: 30)
Exomes 𝑓: 0.0016 ( 17 hom. )
Failed GnomAD Quality Control

Consequence

DICER1
NM_177438.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.425
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6
Variant 14-95099771-C-CACACAA is Benign according to our data. Variant chr14-95099771-C-CACACAA is described in ClinVar as [Benign]. Clinvar id is 242102.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0159 (428/26840) while in subpopulation AFR AF= 0.0274 (379/13832). AF 95% confidence interval is 0.0251. There are 10 homozygotes in gnomad4. There are 212 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 428 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DICER1NM_177438.3 linkc.4206+8_4206+9insTTGTGT splice_region_variant, intron_variant Intron 22 of 26 ENST00000343455.8 NP_803187.1 Q9UPY3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DICER1ENST00000343455.8 linkc.4206+8_4206+9insTTGTGT splice_region_variant, intron_variant Intron 22 of 26 1 NM_177438.3 ENSP00000343745.3 Q9UPY3-1

Frequencies

GnomAD3 genomes
AF:
0.0159
AC:
425
AN:
26760
Hom.:
10
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0273
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0181
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00296
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0286
Gnomad NFE
AF:
0.000423
Gnomad OTH
AF:
0.00971
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00158
AC:
435
AN:
274656
Hom.:
17
Cov.:
34
AF XY:
0.00142
AC XY:
191
AN XY:
134606
show subpopulations
Gnomad4 AFR exome
AF:
0.0217
Gnomad4 AMR exome
AF:
0.00805
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000413
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000258
Gnomad4 OTH exome
AF:
0.00444
GnomAD4 genome
AF:
0.0159
AC:
428
AN:
26840
Hom.:
10
Cov.:
30
AF XY:
0.0163
AC XY:
212
AN XY:
13038
show subpopulations
Gnomad4 AFR
AF:
0.0274
Gnomad4 AMR
AF:
0.0181
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00292
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000423
Gnomad4 OTH
AF:
0.00952

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Jul 09, 2021
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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DICER1-related tumor predisposition Benign:1
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs763704682; hg19: chr14-95566108; API