chr9-127808825-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000373247.7(FPGS):āc.996G>Cā(p.Arg332Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,563,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000373247.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FPGS | NM_004957.6 | c.996G>C | p.Arg332Ser | missense_variant | 11/15 | ENST00000373247.7 | NP_004948.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FPGS | ENST00000373247.7 | c.996G>C | p.Arg332Ser | missense_variant | 11/15 | 1 | NM_004957.6 | ENSP00000362344.2 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000227 AC: 39AN: 171588Hom.: 0 AF XY: 0.000251 AC XY: 23AN XY: 91506
GnomAD4 exome AF: 0.000262 AC: 369AN: 1410844Hom.: 0 Cov.: 32 AF XY: 0.000260 AC XY: 181AN XY: 697324
GnomAD4 genome AF: 0.000243 AC: 37AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.996G>C (p.R332S) alteration is located in exon 11 (coding exon 11) of the FPGS gene. This alteration results from a G to C substitution at nucleotide position 996, causing the arginine (R) at amino acid position 332 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