15-82765182-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001007122.4(FSD2):c.1804G>T(p.Asp602Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,604,232 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D602H) has been classified 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.1804G>T | p.Asp602Tyr | missense_variant | Exon 11 of 13 | 1 | NM_001007122.4 | ENSP00000335651.8 | ||
FSD2 | ENST00000541889.1 | c.1669G>T | p.Asp557Tyr | missense_variant | Exon 10 of 12 | 1 | ENSP00000444078.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242670Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132022
GnomAD4 exome AF: 0.00000551 AC: 8AN: 1452192Hom.: 0 Cov.: 30 AF XY: 0.00000554 AC XY: 4AN XY: 721668
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1804G>T (p.D602Y) alteration is located in exon 11 (coding exon 10) of the FSD2 gene. This alteration results from a G to T substitution at nucleotide position 1804, causing the aspartic acid (D) at amino acid position 602 to be replaced by a tyrosine (Y). 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