chr16-7518294-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_018723.4(RBFOX1):c.175C>T(p.Pro59Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000245 in 1,614,158 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P59P) has been classified as Likely benign.
Frequency
Consequence
NM_018723.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBFOX1 | NM_018723.4 | c.175C>T | p.Pro59Ser | missense_variant | 5/16 | ENST00000550418.6 | |
RBFOX1 | NM_145893.3 | c.235C>T | p.Pro79Ser | missense_variant | 2/14 | ENST00000355637.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBFOX1 | ENST00000550418.6 | c.175C>T | p.Pro59Ser | missense_variant | 5/16 | 1 | NM_018723.4 | A1 | |
RBFOX1 | ENST00000355637.9 | c.235C>T | p.Pro79Ser | missense_variant | 2/14 | 1 | NM_145893.3 |
Frequencies
GnomAD3 genomes AF: 0.00131 AC: 200AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000274 AC: 69AN: 251400Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135876
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727242
GnomAD4 genome AF: 0.00131 AC: 200AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74456
ClinVar
Submissions by phenotype
RBFOX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 13, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Idiopathic generalized epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at