X-151722682-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033085.3(FATE1):c.475C>A(p.Arg159Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000638 in 1,097,798 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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. R159H) has been classified as Uncertain significance.
Frequency
Consequence
NM_033085.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181784Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66934
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1097798Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363206
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.475C>A (p.R159S) alteration is located in exon 5 (coding exon 5) of the FATE1 gene. This alteration results from a C to A substitution at nucleotide position 475, causing the arginine (R) at amino acid position 159 to be replaced by a serine (S). 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