10-96620487-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_152309.3(PIK3AP1):c.1806G>A(p.Thr602Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 1 hom. )
Consequence
PIK3AP1
NM_152309.3 synonymous
NM_152309.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.89
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 10-96620487-C-T is Benign according to our data. Variant chr10-96620487-C-T is described in ClinVar as [Benign]. Clinvar id is 474918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.89 with no splicing effect.
BS2
High AC in GnomAd4 at 104 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.1806G>A | p.Thr602Thr | synonymous_variant | Exon 12 of 17 | ENST00000339364.10 | NP_689522.2 | |
PIK3AP1 | XM_011539248.2 | c.1806G>A | p.Thr602Thr | synonymous_variant | Exon 12 of 16 | XP_011537550.1 | ||
PIK3AP1 | XM_005269499.2 | c.1272G>A | p.Thr424Thr | synonymous_variant | Exon 11 of 16 | XP_005269556.1 | ||
PIK3AP1 | XM_047424566.1 | c.1272G>A | p.Thr424Thr | synonymous_variant | Exon 13 of 18 | XP_047280522.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.1806G>A | p.Thr602Thr | synonymous_variant | Exon 12 of 17 | 1 | NM_152309.3 | ENSP00000339826.5 | ||
PIK3AP1 | ENST00000371109.3 | c.603G>A | p.Thr201Thr | synonymous_variant | Exon 5 of 10 | 1 | ENSP00000360150.3 | |||
PIK3AP1 | ENST00000371110.6 | c.1272G>A | p.Thr424Thr | synonymous_variant | Exon 11 of 16 | 2 | ENSP00000360151.2 | |||
PIK3AP1 | ENST00000489982.1 | n.-76G>A | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000684 AC: 104AN: 152138Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000677 AC: 170AN: 251234Hom.: 0 AF XY: 0.000656 AC XY: 89AN XY: 135768
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GnomAD4 exome AF: 0.00114 AC: 1660AN: 1461774Hom.: 1 Cov.: 34 AF XY: 0.00114 AC XY: 827AN XY: 727190
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GnomAD4 genome AF: 0.000683 AC: 104AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000699 AC XY: 52AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Infantile spasms Benign:1
Jan 13, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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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