10-96602297-C-T
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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.2343G>A(p.Pro781=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000523 in 1,605,850 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 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000054 ( 0 hom. )
Consequence
PIK3AP1
NM_152309.3 synonymous
NM_152309.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.31
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=-0.75).
BP6
Variant 10-96602297-C-T is Benign according to our data. Variant chr10-96602297-C-T is described in ClinVar as [Benign]. Clinvar id is 1170324.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.31 with no splicing effect.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2343G>A | p.Pro781= | synonymous_variant | 16/17 | ENST00000339364.10 | NP_689522.2 | |
LOC105378443 | XR_946220.4 | n.1447-5379C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2343G>A | p.Pro781= | synonymous_variant | 16/17 | 1 | NM_152309.3 | ENSP00000339826 | P1 | |
PIK3AP1 | ENST00000371109.3 | c.1140G>A | p.Pro380= | synonymous_variant | 9/10 | 1 | ENSP00000360150 | |||
PIK3AP1 | ENST00000371110.6 | c.1809G>A | p.Pro603= | synonymous_variant | 15/16 | 2 | ENSP00000360151 | |||
PIK3AP1 | ENST00000467625.5 | n.540G>A | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152146Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000131 AC: 32AN: 243572Hom.: 0 AF XY: 0.000121 AC XY: 16AN XY: 131874
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GnomAD4 exome AF: 0.0000537 AC: 78AN: 1453586Hom.: 0 Cov.: 30 AF XY: 0.0000567 AC XY: 41AN XY: 723198
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74454
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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