rs11204980
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002016.2(FLG):c.-22+1474C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,152 control chromosomes in the GnomAD database, including 4,049 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 4049 hom., cov: 31)
Consequence
FLG
NM_002016.2 intron
NM_002016.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.835
Publications
6 publications found
Genes affected
FLG (HGNC:3748): (filaggrin) The protein encoded by this gene is an intermediate filament-associated protein that aggregates keratin intermediate filaments in mammalian epidermis. It is initially synthesized as a polyprotein precursor, profilaggrin (consisting of multiple filaggrin units of 324 aa each), which is localized in keratohyalin granules, and is subsequently proteolytically processed into individual functional filaggrin molecules. Mutations in this gene are associated with ichthyosis vulgaris.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.202 AC: 30553AN: 151036Hom.: 4041 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
30553
AN:
151036
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.202 AC: 30574AN: 151152Hom.: 4049 Cov.: 31 AF XY: 0.214 AC XY: 15777AN XY: 73828 show subpopulations
GnomAD4 genome
AF:
AC:
30574
AN:
151152
Hom.:
Cov.:
31
AF XY:
AC XY:
15777
AN XY:
73828
show subpopulations
African (AFR)
AF:
AC:
5493
AN:
41276
American (AMR)
AF:
AC:
5422
AN:
15134
Ashkenazi Jewish (ASJ)
AF:
AC:
1088
AN:
3460
East Asian (EAS)
AF:
AC:
3047
AN:
5106
South Asian (SAS)
AF:
AC:
2087
AN:
4806
European-Finnish (FIN)
AF:
AC:
1967
AN:
10474
Middle Eastern (MID)
AF:
AC:
79
AN:
292
European-Non Finnish (NFE)
AF:
AC:
10732
AN:
67602
Other (OTH)
AF:
AC:
480
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1125
2249
3374
4498
5623
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1753
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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