rs149081991
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005027.4(PIK3R2):c.2179G>A(p.Ala727Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 1,495,138 control chromosomes in the GnomAD database, including 1,847 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005027.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3R2 | NM_005027.4 | c.2179G>A | p.Ala727Thr | missense_variant | 16/16 | ENST00000222254.13 | NP_005018.2 | |
PIK3R2 | NR_073517.2 | n.2783G>A | non_coding_transcript_exon_variant | 16/16 | ||||
PIK3R2 | NR_162071.1 | n.2521G>A | non_coding_transcript_exon_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3R2 | ENST00000222254.13 | c.2179G>A | p.Ala727Thr | missense_variant | 16/16 | 1 | NM_005027.4 | ENSP00000222254 | P1 | |
PIK3R2 | ENST00000617130.5 | c.*1207G>A | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 1 | ENSP00000477864 | ||||
PIK3R2 | ENST00000426902.5 | c.*782G>A | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 2 | ENSP00000395636 | ||||
PIK3R2 | ENST00000617642.2 | c.*1207G>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 5 | ENSP00000484714 |
Frequencies
GnomAD3 genomes AF: 0.0383 AC: 5819AN: 151832Hom.: 151 Cov.: 33
GnomAD3 exomes AF: 0.0420 AC: 4305AN: 102418Hom.: 150 AF XY: 0.0411 AC XY: 2330AN XY: 56684
GnomAD4 exome AF: 0.0451 AC: 60598AN: 1343198Hom.: 1696 Cov.: 31 AF XY: 0.0446 AC XY: 29493AN XY: 661842
GnomAD4 genome AF: 0.0383 AC: 5818AN: 151940Hom.: 151 Cov.: 33 AF XY: 0.0400 AC XY: 2974AN XY: 74278
ClinVar
Submissions by phenotype
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at