rs1555815294
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005027.4(PIK3R2):āc.2093A>Cā(p.His698Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. H698H) has been classified as Likely benign.
Frequency
Consequence
NM_005027.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R2 | NM_005027.4 | c.2093A>C | p.His698Pro | missense_variant | 16/16 | ENST00000222254.13 | |
PIK3R2 | NR_073517.2 | n.2697A>C | non_coding_transcript_exon_variant | 16/16 | |||
PIK3R2 | NR_162071.1 | n.2435A>C | non_coding_transcript_exon_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R2 | ENST00000222254.13 | c.2093A>C | p.His698Pro | missense_variant | 16/16 | 1 | NM_005027.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454656Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723932
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Choreoathetosis;C0266476:Aqueductal stenosis;C0557874:Global developmental delay Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Personalized Medicine, Children's Hospital Los Angeles | Mar 15, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at