chr9-127802988-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004957.6(FPGS):āc.64A>Gā(p.Ile22Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 1,461,332 control chromosomes in the GnomAD database, including 331,092 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPGS | NM_004957.6 | c.64A>G | p.Ile22Val | missense_variant | 1/15 | ENST00000373247.7 | |
FPGS | NM_001288803.1 | c.64A>G | p.Ile22Val | missense_variant | 1/14 | ||
FPGS | XM_005251864.5 | c.64A>G | p.Ile22Val | missense_variant | 1/16 | ||
FPGS | NR_110170.1 | n.131A>G | non_coding_transcript_exon_variant | 1/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPGS | ENST00000373247.7 | c.64A>G | p.Ile22Val | missense_variant | 1/15 | 1 | NM_004957.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.728 AC: 110439AN: 151712Hom.: 41131 Cov.: 31
GnomAD3 exomes AF: 0.638 AC: 42882AN: 67242Hom.: 14001 AF XY: 0.639 AC XY: 25003AN XY: 39114
GnomAD4 exome AF: 0.662 AC: 866421AN: 1309512Hom.: 289921 Cov.: 56 AF XY: 0.662 AC XY: 426723AN XY: 645006
GnomAD4 genome AF: 0.728 AC: 110528AN: 151820Hom.: 41171 Cov.: 31 AF XY: 0.731 AC XY: 54217AN XY: 74176
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 29, 2020 | This variant is associated with the following publications: (PMID: 25765001) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at