15-82765927-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001007122.4(FSD2):c.1658G>A(p.Arg553Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,610,400 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_001007122.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSD2 | ENST00000334574.12 | c.1658G>A | p.Arg553Lys | missense_variant | Exon 10 of 13 | 1 | NM_001007122.4 | ENSP00000335651.8 | ||
FSD2 | ENST00000541889.1 | c.1523G>A | p.Arg508Lys | missense_variant | Exon 9 of 12 | 1 | ENSP00000444078.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242428Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131614
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458180Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725024
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1658G>A (p.R553K) alteration is located in exon 10 (coding exon 9) of the FSD2 gene. This alteration results from a G to A substitution at nucleotide position 1658, causing the arginine (R) at amino acid position 553 to be replaced by a lysine (K). 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