rs569632623
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_152309.3(PIK3AP1):c.2186G>A(p.Arg729His) variant causes a missense change. The variant allele was found at a frequency of 0.000125 in 1,604,524 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R729C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2186G>A | p.Arg729His | missense_variant | 15/17 | ENST00000339364.10 | |
LOC105378443 | XR_946220.4 | n.1447-3642C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2186G>A | p.Arg729His | missense_variant | 15/17 | 1 | NM_152309.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152138Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000660 AC: 156AN: 236420Hom.: 0 AF XY: 0.000440 AC XY: 56AN XY: 127342
GnomAD4 exome AF: 0.000126 AC: 183AN: 1452268Hom.: 0 Cov.: 30 AF XY: 0.000111 AC XY: 80AN XY: 721706
GnomAD4 genome AF: 0.000112 AC: 17AN: 152256Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74440
ClinVar
Submissions by phenotype
Infantile spasms Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
PIK3AP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2022 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at