chr16-6044556-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018723.4(RBFOX1):c.-127+24564C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,556 control chromosomes in the GnomAD database, including 5,319 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 0.25 ( 5319 hom., cov: 32)
Consequence
RBFOX1
NM_018723.4 intron
NM_018723.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.165
Publications
2 publications found
Genes affected
RBFOX1 (HGNC:18222): (RNA binding fox-1 homolog 1) The Fox-1 family of RNA-binding proteins is evolutionarily conserved, and regulates tissue-specific alternative splicing in metazoa. Fox-1 recognizes a (U)GCAUG stretch in regulated exons or in flanking introns. The protein binds to the C-terminus of ataxin-2 and may contribute to the restricted pathology of spinocerebellar ataxia type 2 (SCA2). Ataxin-2 is the product of the SCA2 gene which causes familial neurodegenerative diseases. Fox-1 and ataxin-2 are both localized in the trans-Golgi network. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
RBFOX1 Gene-Disease associations (from GenCC):
- epilepsyInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: G2P
- autism susceptibility 1Inheritance: Unknown Classification: LIMITED Submitted by: Laboratory for Molecular Medicine
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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=-0.55).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.248 AC: 37610AN: 151480Hom.: 5321 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
37610
AN:
151480
Hom.:
Cov.:
32
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: 0.248 AC: 37600AN: 151556Hom.: 5319 Cov.: 32 AF XY: 0.246 AC XY: 18182AN XY: 73968 show subpopulations
GnomAD4 genome
AF:
AC:
37600
AN:
151556
Hom.:
Cov.:
32
AF XY:
AC XY:
18182
AN XY:
73968
show subpopulations
African (AFR)
AF:
AC:
4496
AN:
41310
American (AMR)
AF:
AC:
4242
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
AC:
893
AN:
3466
East Asian (EAS)
AF:
AC:
1020
AN:
5136
South Asian (SAS)
AF:
AC:
1388
AN:
4784
European-Finnish (FIN)
AF:
AC:
2951
AN:
10442
Middle Eastern (MID)
AF:
AC:
64
AN:
286
European-Non Finnish (NFE)
AF:
AC:
21649
AN:
67908
Other (OTH)
AF:
AC:
526
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1398
2795
4193
5590
6988
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
396
792
1188
1584
1980
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
790
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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