rs1941526
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002647.4(PIK3C3):c.2649+5462C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,068 control chromosomes in the GnomAD database, including 5,064 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5064 hom., cov: 32)
Consequence
PIK3C3
NM_002647.4 intron
NM_002647.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.556
Genes affected
PIK3C3 (HGNC:8974): (phosphatidylinositol 3-kinase catalytic subunit type 3) Enables 1-phosphatidylinositol-3-kinase activity. Involved in early endosome to late endosome transport and regulation of cytokinesis. Acts upstream of or within autophagy and protein lipidation. Located in autolysosome; late endosome; and midbody. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C3 | NM_002647.4 | c.2649+5462C>T | intron_variant | ENST00000262039.9 | |||
PIK3C3 | NM_001308020.2 | c.2460+5462C>T | intron_variant | ||||
PIK3C3 | XM_047437550.1 | c.2091+5462C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C3 | ENST00000262039.9 | c.2649+5462C>T | intron_variant | 1 | NM_002647.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.252 AC: 38290AN: 151950Hom.: 5067 Cov.: 32
GnomAD3 genomes
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38290
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151950
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.252 AC: 38302AN: 152068Hom.: 5064 Cov.: 32 AF XY: 0.255 AC XY: 18937AN XY: 74354
GnomAD4 genome
?
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38302
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152068
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32
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18937
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74354
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1270
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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