chr17-7593073-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004860.4(FXR2):c.1439G>C(p.Ser480Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000377 in 1,591,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004860.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXR2 | NM_004860.4 | c.1439G>C | p.Ser480Thr | missense_variant | 13/17 | ENST00000250113.12 | |
FXR2 | XM_047437106.1 | c.1439G>C | p.Ser480Thr | missense_variant | 13/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXR2 | ENST00000250113.12 | c.1439G>C | p.Ser480Thr | missense_variant | 13/17 | 1 | NM_004860.4 | P1 | |
FXR2 | ENST00000704984.1 | c.1658G>C | p.Ser553Thr | missense_variant | 13/17 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000442 AC: 1AN: 226178Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123468
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1439500Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 715562
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1439G>C (p.S480T) alteration is located in exon 13 (coding exon 13) of the FXR2 gene. This alteration results from a G to C substitution at nucleotide position 1439, causing the serine (S) at amino acid position 480 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