Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001350451.2(RBFOX3):c.998+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000981 in 1,550,510 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
RBFOX3 (HGNC:27097): (RNA binding fox-1 homolog 3) This gene encodes a member of the RNA-binding FOX protein family which is involved in the regulation of alternative splicing of pre-mRNA. The protein has an N-terminal proline-rich region, an RNA recognition motif (RRM) domain, and a C-terminal alanine-rich region. This gene produces the neuronal nuclei (NeuN) antigen that has been widely used as a marker for post-mitotic neurons. This gene has its highest expression in the central nervous system and plays a prominent role in neural tissue development and regulation of adult brain function. Mutations in this gene have been associated with numerous neurological disorders. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2017]
RBFOX3 Gene-Disease associations (from GenCC):
epilepsy
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 17-79095504-C-A is Benign according to our data. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-79095504-C-A is described in CliVar as Benign. Clinvar id is 416625.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00566 (862/152340) while in subpopulation AFR AF = 0.0197 (820/41580). AF 95% confidence interval is 0.0186. There are 9 homozygotes in GnomAd4. There are 444 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -