9-127802952-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004957.6(FPGS):c.28G>T(p.Ala10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004957.6 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.28G>T | p.Ala10Ser | missense_variant | 1/15 | ENST00000373247.7 | NP_004948.4 | |
FPGS | NM_001288803.1 | c.28G>T | p.Ala10Ser | missense_variant | 1/14 | NP_001275732.1 | ||
FPGS | XM_005251864.5 | c.28G>T | p.Ala10Ser | missense_variant | 1/16 | XP_005251921.1 | ||
FPGS | NR_110170.1 | n.95G>T | non_coding_transcript_exon_variant | 1/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FPGS | ENST00000373247.7 | c.28G>T | p.Ala10Ser | missense_variant | 1/15 | 1 | NM_004957.6 | ENSP00000362344.2 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1259278Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 616202
GnomAD4 genome Cov.: 29
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 11, 2024 | The c.28G>T (p.A10S) alteration is located in exon 1 (coding exon 1) of the FPGS gene. This alteration results from a G to T substitution at nucleotide position 28, causing the alanine (A) at amino acid position 10 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
Publications
No publications associated with this variant yet.