chr19-18155936-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_005027.4(PIK3R2):c.57G>A(p.Arg19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R19R) has been classified as Likely benign.
Frequency
Consequence
NM_005027.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R2 | NM_005027.4 | c.57G>A | p.Arg19= | synonymous_variant | 2/16 | ENST00000222254.13 | |
PIK3R2 | NR_073517.2 | n.612G>A | non_coding_transcript_exon_variant | 2/16 | |||
PIK3R2 | NR_162071.1 | n.612G>A | non_coding_transcript_exon_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R2 | ENST00000222254.13 | c.57G>A | p.Arg19= | synonymous_variant | 2/16 | 1 | NM_005027.4 | P1 | |
PIK3R2 | ENST00000617130.5 | c.57G>A | p.Arg19= | synonymous_variant, NMD_transcript_variant | 2/15 | 1 | |||
PIK3R2 | ENST00000426902.5 | c.57G>A | p.Arg19= | synonymous_variant, NMD_transcript_variant | 1/15 | 2 | |||
PIK3R2 | ENST00000617642.2 | c.57G>A | p.Arg19= | synonymous_variant, NMD_transcript_variant | 2/14 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1418090Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 701702
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.