rs376060745
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001350451.2(RBFOX3):c.19C>T(p.Pro7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P7L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001350451.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBFOX3 | NM_001350451.2 | c.19C>T | p.Pro7Ser | missense_variant | 5/15 | ENST00000693108.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBFOX3 | ENST00000693108.1 | c.19C>T | p.Pro7Ser | missense_variant | 5/15 | NM_001350451.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 52AN: 151710Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.000117 AC: 10AN: 85296Hom.: 0 AF XY: 0.0000656 AC XY: 3AN XY: 45720
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000836 AC: 53AN: 634050Hom.: 5 Cov.: 9 AF XY: 0.0000932 AC XY: 31AN XY: 332634
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000342 AC: 52AN: 151826Hom.: 0 Cov.: 31 AF XY: 0.000350 AC XY: 26AN XY: 74196
ClinVar
Submissions by phenotype
Idiopathic generalized epilepsy Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at