rs4451422
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_005251864.5(FPGS):c.*91A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 226,298 control chromosomes in the GnomAD database, including 20,447 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 13829 hom., cov: 32)
Exomes 𝑓: 0.41 ( 6618 hom. )
Consequence
FPGS
XM_005251864.5 3_prime_UTR
XM_005251864.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.443
Genes affected
FPGS (HGNC:3824): (folylpolyglutamate synthase) This gene encodes the folylpolyglutamate synthetase enzyme. This enzyme has a central role in establishing and maintaining both cytosolic and mitochondrial folylpolyglutamate concentrations and, therefore, is essential for folate homeostasis and the survival of proliferating cells. This enzyme catalyzes the ATP-dependent addition of glutamate moieties to folate and folate derivatives. Alternative splicing results in transcript variants encoding different isoforms. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPGS | XM_005251864.5 | c.*91A>C | 3_prime_UTR_variant | 16/16 | |||
FPGS | XM_047423127.1 | c.*91A>C | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPGS | ENST00000467826.5 | n.820A>C | non_coding_transcript_exon_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.423 AC: 64218AN: 151906Hom.: 13815 Cov.: 32
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GnomAD4 exome AF: 0.412 AC: 30601AN: 74274Hom.: 6618 Cov.: 4 AF XY: 0.411 AC XY: 14668AN XY: 35674
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GnomAD4 genome ? AF: 0.423 AC: 64276AN: 152024Hom.: 13829 Cov.: 32 AF XY: 0.419 AC XY: 31112AN XY: 74324
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at