rs2139512
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002703.5(PPAT):c.129-2737C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 914,172 control chromosomes in the GnomAD database, including 207,739 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 0.69 ( 35988 hom., cov: 30)
Exomes 𝑓: 0.67 ( 171751 hom. )
Consequence
PPAT
NM_002703.5 intron
NM_002703.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.90
Genes affected
PPAT (HGNC:9238): (phosphoribosyl pyrophosphate amidotransferase) The protein encoded by this gene is a member of the purine/pyrimidine phosphoribosyltransferase family. It is a regulatory allosteric enzyme that catalyzes the first step of de novo purine nucleotide biosythetic pathway. This gene and PAICS/AIRC gene, a bifunctional enzyme catalyzing steps six and seven of this pathway, are located in close proximity on chromosome 4, and divergently transcribed from an intergenic region. [provided by RefSeq, Mar 2011]
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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=-0.53).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPAT | NM_002703.5 | c.129-2737C>G | intron_variant | ENST00000264220.6 | |||
PPAT | NR_156493.2 | n.267-2737C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPAT | ENST00000264220.6 | c.129-2737C>G | intron_variant | 1 | NM_002703.5 | P1 | |||
PPAT | ENST00000507724.1 | c.129-2737C>G | intron_variant, NMD_transcript_variant | 3 | |||||
PPAT | ENST00000510643.5 | c.129-2737C>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.687 AC: 104316AN: 151792Hom.: 35952 Cov.: 30
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GnomAD4 exome AF: 0.671 AC: 511471AN: 762264Hom.: 171751 AF XY: 0.671 AC XY: 237331AN XY: 353842
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GnomAD4 genome ? AF: 0.687 AC: 104412AN: 151908Hom.: 35988 Cov.: 30 AF XY: 0.694 AC XY: 51525AN XY: 74256
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at