rs201568661
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005027.4(PIK3R2):c.1845G>A(p.Pro615=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,549,024 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P615P) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R2 | NM_005027.4 | c.1845G>A | p.Pro615= | synonymous_variant | 15/16 | ENST00000222254.13 | |
PIK3R2 | NR_073517.2 | n.2449G>A | non_coding_transcript_exon_variant | 15/16 | |||
PIK3R2 | NR_162071.1 | n.2187G>A | non_coding_transcript_exon_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R2 | ENST00000222254.13 | c.1845G>A | p.Pro615= | synonymous_variant | 15/16 | 1 | NM_005027.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000741 AC: 11AN: 148408Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000493 AC: 121AN: 245434Hom.: 0 AF XY: 0.000293 AC XY: 39AN XY: 133090
GnomAD4 exome AF: 0.000144 AC: 202AN: 1400482Hom.: 0 Cov.: 38 AF XY: 0.000112 AC XY: 78AN XY: 697016
GnomAD4 genome ? AF: 0.0000741 AC: 11AN: 148542Hom.: 0 Cov.: 32 AF XY: 0.0000689 AC XY: 5AN XY: 72596
ClinVar
Submissions by phenotype
PIK3R2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 27, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at