rs201824606
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_152309.3(PIK3AP1):c.2379C>T(p.Thr793=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,613,146 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 Benign (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
PIK3AP1
NM_152309.3 synonymous
NM_152309.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.897
Genes affected
PIK3AP1 (HGNC:30034): (phosphoinositide-3-kinase adaptor protein 1) Predicted to enable phosphatidylinositol 3-kinase regulatory subunit binding activity and signaling receptor binding activity. Predicted to be involved in regulation of inflammatory response; regulation of signal transduction; and toll-like receptor signaling pathway. Predicted to be located in cytoplasm and membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 10-96595616-G-A is Benign according to our data. Variant chr10-96595616-G-A is described in ClinVar as [Benign]. Clinvar id is 474928.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.897 with no splicing effect.
BS2
?
High AC in GnomAd4 at 45 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2379C>T | p.Thr793= | synonymous_variant | 17/17 | ENST00000339364.10 | |
LOC105378443 | XR_946220.4 | n.1446+4032G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2379C>T | p.Thr793= | synonymous_variant | 17/17 | 1 | NM_152309.3 | P1 | |
PIK3AP1 | ENST00000371109.3 | c.1176C>T | p.Thr392= | synonymous_variant | 10/10 | 1 | |||
PIK3AP1 | ENST00000371110.6 | c.1845C>T | p.Thr615= | synonymous_variant | 16/16 | 2 | |||
PIK3AP1 | ENST00000467625.5 | n.576C>T | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152156Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000298 AC: 74AN: 248206Hom.: 0 AF XY: 0.000299 AC XY: 40AN XY: 133884
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GnomAD4 exome AF: 0.000215 AC: 314AN: 1460990Hom.: 0 Cov.: 30 AF XY: 0.000206 AC XY: 150AN XY: 726740
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GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Infantile spasms Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at