9-127803013-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004957.6(FPGS):c.89G>A(p.Arg30Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000614 in 1,465,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FPGS | NM_004957.6 | c.89G>A | p.Arg30Gln | missense_variant | Exon 1 of 15 | ENST00000373247.7 | NP_004948.4 | |
FPGS | NM_001288803.1 | c.89G>A | p.Arg30Gln | missense_variant | Exon 1 of 14 | NP_001275732.1 | ||
FPGS | XM_005251864.5 | c.89G>A | p.Arg30Gln | missense_variant | Exon 1 of 16 | XP_005251921.1 | ||
FPGS | NR_110170.1 | n.156G>A | non_coding_transcript_exon_variant | Exon 1 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000581 AC: 4AN: 68814Hom.: 0 AF XY: 0.0000751 AC XY: 3AN XY: 39936
GnomAD4 exome AF: 0.00000457 AC: 6AN: 1313362Hom.: 0 Cov.: 35 AF XY: 0.00000773 AC XY: 5AN XY: 647080
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.89G>A (p.R30Q) alteration is located in exon 1 (coding exon 1) of the FPGS gene. This alteration results from a G to A substitution at nucleotide position 89, causing the arginine (R) at amino acid position 30 to be replaced by a glutamine (Q). 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