rs797044528
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_023067.4(FOXL2):c.804delC(p.Gly269AlafsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FOXL2
NM_023067.4 frameshift
NM_023067.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.636
Genes affected
FOXL2 (HGNC:1092): (forkhead box L2) This gene encodes a forkhead transcription factor. The protein contains a fork-head DNA-binding domain and may play a role in ovarian development and function. Expansion of a polyalanine repeat region and other mutations in this gene are a cause of blepharophimosis syndrome and premature ovarian failure 3. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 10 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 26 pathogenic variants in the truncated region.
PP5
Variant 3-138945918-CG-C is Pathogenic according to our data. Variant chr3-138945918-CG-C is described in ClinVar as [Pathogenic]. Clinvar id is 369930.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150810Hom.: 0 Cov.: 32
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GnomAD2 exomes AF: 0.0000834 AC: 5AN: 59924 AF XY: 0.000115 show subpopulations
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000338 AC: 4AN: 1184666Hom.: 0 Cov.: 31 AF XY: 0.00000525 AC XY: 3AN XY: 571578 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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⚠️ The allele balance in gnomAD4 Exomes is highly skewed (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
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Allele balance
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 150810Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73604
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Data not reliable, filtered out with message: AC0;AS_VQSR
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Blepharophimosis, ptosis, and epicanthus inversus syndrome Pathogenic:2
Nov 03, 2016
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Jan 01, 2015
Wessex Regional Genetics Laboratory, Salisbury District Hospital
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing
- -
Computational scores
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Name
Calibrated prediction
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Prediction
Mutation Taster
=7/193
disease causing (ClinVar)
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at