17-7593022-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004860.4(FXR2):c.1490G>A(p.Arg497Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,576,774 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R497W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004860.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXR2 | NM_004860.4 | c.1490G>A | p.Arg497Gln | missense_variant | 13/17 | ENST00000250113.12 | |
FXR2 | XM_047437106.1 | c.1490G>A | p.Arg497Gln | missense_variant | 13/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXR2 | ENST00000250113.12 | c.1490G>A | p.Arg497Gln | missense_variant | 13/17 | 1 | NM_004860.4 | P1 | |
FXR2 | ENST00000704984.1 | c.1709G>A | p.Arg570Gln | missense_variant | 13/17 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000285 AC: 6AN: 210878Hom.: 0 AF XY: 0.0000174 AC XY: 2AN XY: 114990
GnomAD4 exome AF: 0.000119 AC: 169AN: 1424810Hom.: 0 Cov.: 32 AF XY: 0.000117 AC XY: 83AN XY: 706986
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74202
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.1490G>A (p.R497Q) alteration is located in exon 13 (coding exon 13) of the FXR2 gene. This alteration results from a G to A substitution at nucleotide position 1490, causing the arginine (R) at amino acid position 497 to be replaced by a glutamine (Q). 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