rs9903447
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142633.3(PIK3R5):c.2299+18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,612,248 control chromosomes in the GnomAD database, including 54,025 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.28 ( 6770 hom., cov: 31)
Exomes 𝑓: 0.25 ( 47255 hom. )
Consequence
PIK3R5
NM_001142633.3 intron
NM_001142633.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.633
Genes affected
PIK3R5 (HGNC:30035): (phosphoinositide-3-kinase regulatory subunit 5) Phosphatidylinositol 3-kinases (PI3Ks) phosphorylate the inositol ring of phosphatidylinositol at the 3-prime position, and play important roles in cell growth, proliferation, differentiation, motility, survival and intracellular trafficking. The PI3Ks are divided into three classes: I, II and III, and only the class I PI3Ks are involved in oncogenesis. This gene encodes the 101 kD regulatory subunit of the class I PI3K gamma complex, which is a dimeric enzyme, consisting of a 110 kD catalytic subunit gamma and a regulatory subunit of either 55, 87 or 101 kD. This protein recruits the catalytic subunit from the cytosol to the plasma membrane through high-affinity interaction with G-beta-gamma proteins. Multiple alternatively spliced transcript variants encoding two distinct isoforms have been found. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 17-8881770-A-C is Benign according to our data. Variant chr17-8881770-A-C is described in ClinVar as [Benign]. Clinvar id is 257557.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-8881770-A-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R5 | NM_001142633.3 | c.2299+18T>G | intron_variant | ENST00000447110.6 | |||
LOC124903919 | XR_007065610.1 | n.924-2796A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R5 | ENST00000447110.6 | c.2299+18T>G | intron_variant | 5 | NM_001142633.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.281 AC: 42534AN: 151490Hom.: 6764 Cov.: 31
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GnomAD3 exomes AF: 0.222 AC: 55607AN: 250724Hom.: 7173 AF XY: 0.215 AC XY: 29107AN XY: 135516
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GnomAD4 exome AF: 0.247 AC: 360117AN: 1460640Hom.: 47255 Cov.: 32 AF XY: 0.241 AC XY: 175485AN XY: 726682
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GnomAD4 genome ? AF: 0.281 AC: 42568AN: 151608Hom.: 6770 Cov.: 31 AF XY: 0.271 AC XY: 20036AN XY: 74048
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ataxia with oculomotor apraxia type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
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