chr10-96602261-A-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152309.3(PIK3AP1):c.2360+19T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,563,552 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 (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
PIK3AP1
NM_152309.3 intron
NM_152309.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.883
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 10-96602261-A-T is Benign according to our data. Variant chr10-96602261-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1591470.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 29 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2360+19T>A | intron_variant | ENST00000339364.10 | NP_689522.2 | |||
LOC105378443 | XR_946220.4 | n.1447-5415A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2360+19T>A | intron_variant | 1 | NM_152309.3 | ENSP00000339826 | P1 | |||
PIK3AP1 | ENST00000371109.3 | c.1157+19T>A | intron_variant | 1 | ENSP00000360150 | |||||
PIK3AP1 | ENST00000371110.6 | c.1826+19T>A | intron_variant | 2 | ENSP00000360151 | |||||
PIK3AP1 | ENST00000467625.5 | n.557+19T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151942Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241138Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130572
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GnomAD4 exome AF: 0.0000205 AC: 29AN: 1411610Hom.: 0 Cov.: 26 AF XY: 0.0000185 AC XY: 13AN XY: 704524
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151942Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74206
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Infantile spasms Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at