19-18155921-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_005027.4(PIK3R2):c.42G>A(p.Pro14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,566,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P14P) has been classified as Likely benign.
Frequency
Consequence
NM_005027.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R2 | NM_005027.4 | c.42G>A | p.Pro14= | synonymous_variant | 2/16 | ENST00000222254.13 | |
PIK3R2 | NR_073517.2 | n.597G>A | non_coding_transcript_exon_variant | 2/16 | |||
PIK3R2 | NR_162071.1 | n.597G>A | non_coding_transcript_exon_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R2 | ENST00000222254.13 | c.42G>A | p.Pro14= | synonymous_variant | 2/16 | 1 | NM_005027.4 | P1 | |
PIK3R2 | ENST00000617130.5 | c.42G>A | p.Pro14= | synonymous_variant, NMD_transcript_variant | 2/15 | 1 | |||
PIK3R2 | ENST00000426902.5 | c.42G>A | p.Pro14= | synonymous_variant, NMD_transcript_variant | 1/15 | 2 | |||
PIK3R2 | ENST00000617642.2 | c.42G>A | p.Pro14= | synonymous_variant, NMD_transcript_variant | 2/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000117 AC: 2AN: 170512Hom.: 0 AF XY: 0.0000108 AC XY: 1AN XY: 92652
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1414182Hom.: 0 Cov.: 31 AF XY: 0.00000858 AC XY: 6AN XY: 699458
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at