chr3-138818180-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006219.3(PIK3CB):​c.-122+16515C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,878 control chromosomes in the GnomAD database, including 14,154 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 0.42 ( 14154 hom., cov: 31)

Consequence

PIK3CB
NM_006219.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.577
Variant links:
Genes affected
PIK3CB (HGNC:8976): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) This gene encodes an isoform of the catalytic subunit of phosphoinositide 3-kinase (PI3K). These kinases are important in signaling pathways involving receptors on the outer membrane of eukaryotic cells and are named for their catalytic subunit. The encoded protein is the catalytic subunit for PI3Kbeta (PI3KB). PI3KB has been shown to be part of the activation pathway in neutrophils which have bound immune complexes at sites of injury or infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]

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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 (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIK3CBNM_006219.3 linkuse as main transcriptc.-122+16515C>G intron_variant ENST00000674063.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3CBENST00000674063.1 linkuse as main transcriptc.-122+16515C>G intron_variant NM_006219.3 P1
PIK3CBENST00000477593.5 linkuse as main transcriptc.-17+16515C>G intron_variant 5 P1
PIK3CBENST00000483968.5 linkuse as main transcriptc.-189+16515C>G intron_variant 3
PIK3CBENST00000462898.5 linkuse as main transcriptc.-17+16515C>G intron_variant, NMD_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.419
AC:
63613
AN:
151760
Hom.:
14152
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.436
Gnomad AMI
AF:
0.546
Gnomad AMR
AF:
0.348
Gnomad ASJ
AF:
0.518
Gnomad EAS
AF:
0.0154
Gnomad SAS
AF:
0.342
Gnomad FIN
AF:
0.337
Gnomad MID
AF:
0.503
Gnomad NFE
AF:
0.466
Gnomad OTH
AF:
0.444
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.419
AC:
63633
AN:
151878
Hom.:
14154
Cov.:
31
AF XY:
0.408
AC XY:
30251
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.435
Gnomad4 AMR
AF:
0.348
Gnomad4 ASJ
AF:
0.518
Gnomad4 EAS
AF:
0.0153
Gnomad4 SAS
AF:
0.342
Gnomad4 FIN
AF:
0.337
Gnomad4 NFE
AF:
0.466
Gnomad4 OTH
AF:
0.439
Alfa
AF:
0.269
Hom.:
612
Bravo
AF:
0.419
Asia WGS
AF:
0.185
AC:
644
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.58
DANN
Benign
0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6784610; hg19: chr3-138537022; API