rs760198924
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001349999.2(RBFOX2):c.1192G>A(p.Ala398Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000628 in 1,609,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001349999.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBFOX2 | NM_001349999.2 | c.1192G>A | p.Ala398Thr | missense_variant | Exon 12 of 14 | ENST00000695854.1 | NP_001336928.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBFOX2 | ENST00000695854.1 | c.1192G>A | p.Ala398Thr | missense_variant | Exon 12 of 14 | NM_001349999.2 | ENSP00000512219.1 | |||
RBFOX2 | ENST00000438146.7 | c.1204G>A | p.Ala402Thr | missense_variant | Exon 12 of 14 | 1 | ENSP00000413035.2 | |||
RBFOX2 | ENST00000449924.6 | c.991G>A | p.Ala331Thr | missense_variant | Exon 11 of 13 | 1 | ENSP00000391670.2 | |||
RBFOX2 | ENST00000414461.6 | c.951G>A | p.Pro317Pro | synonymous_variant | Exon 10 of 12 | 1 | ENSP00000407855.2 | |||
RBFOX2 | ENST00000695805.1 | n.*485G>A | non_coding_transcript_exon_variant | Exon 11 of 13 | ENSP00000512185.1 | |||||
RBFOX2 | ENST00000695807.1 | n.*4175G>A | non_coding_transcript_exon_variant | Exon 13 of 15 | ENSP00000512187.1 | |||||
RBFOX2 | ENST00000695805.1 | n.*485G>A | 3_prime_UTR_variant | Exon 11 of 13 | ENSP00000512185.1 | |||||
RBFOX2 | ENST00000695807.1 | n.*4175G>A | 3_prime_UTR_variant | Exon 13 of 15 | ENSP00000512187.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000286 AC: 7AN: 244550Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132574
GnomAD4 exome AF: 0.0000679 AC: 99AN: 1457222Hom.: 0 Cov.: 30 AF XY: 0.0000759 AC XY: 55AN XY: 725048
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1204G>A (p.A402T) alteration is located in exon 12 (coding exon 12) of the RBFOX2 gene. This alteration results from a G to A substitution at nucleotide position 1204, causing the alanine (A) at amino acid position 402 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at