rs11077813
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002766.3(PRPSAP1):c.290+4207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,394 control chromosomes in the GnomAD database, including 4,284 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 0.21 ( 4284 hom., cov: 32)
Consequence
PRPSAP1
NM_002766.3 intron
NM_002766.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.45
Genes affected
PRPSAP1 (HGNC:9466): (phosphoribosyl pyrophosphate synthetase associated protein 1) Enables identical protein binding activity. Predicted to be involved in 5-phosphoribose 1-diphosphate biosynthetic process and purine nucleotide biosynthetic process. Predicted to be part of ribose phosphate diphosphokinase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPSAP1 | NM_002766.3 | c.290+4207A>G | intron_variant | ENST00000446526.8 | NP_002757.2 | |||
PRPSAP1 | NM_001330503.2 | c.-19-8029A>G | intron_variant | NP_001317432.1 | ||||
PRPSAP1 | NM_001366236.2 | c.-20+4207A>G | intron_variant | NP_001353165.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.207 AC: 31271AN: 151276Hom.: 4287 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.206 AC: 31261AN: 151394Hom.: 4284 Cov.: 32 AF XY: 0.212 AC XY: 15697AN XY: 74000
GnomAD4 genome
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74000
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1239
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3478
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