15-82765931-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001007122.4(FSD2):c.1654G>A(p.Val552Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,610,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSD2 | ENST00000334574.12 | c.1654G>A | p.Val552Met | missense_variant | Exon 10 of 13 | 1 | NM_001007122.4 | ENSP00000335651.8 | ||
FSD2 | ENST00000541889.1 | c.1519G>A | p.Val507Met | missense_variant | Exon 9 of 12 | 1 | ENSP00000444078.1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000869 AC: 21AN: 241752Hom.: 0 AF XY: 0.000107 AC XY: 14AN XY: 131232
GnomAD4 exome AF: 0.000169 AC: 246AN: 1457974Hom.: 0 Cov.: 31 AF XY: 0.000182 AC XY: 132AN XY: 724880
GnomAD4 genome AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1654G>A (p.V552M) 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 1654, causing the valine (V) at amino acid position 552 to be replaced by a methionine (M). 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