rs4855094

Variant summary

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

The NM_006218.4(PIK3CA):​c.-77+11586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,176 control chromosomes in the GnomAD database, including 1,186 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 0.099 ( 1186 hom., cov: 32)

Consequence

PIK3CA
NM_006218.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259
Variant links:
Genes affected
PIK3CA (HGNC:8975): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) Phosphatidylinositol 3-kinase is composed of an 85 kDa regulatory subunit and a 110 kDa catalytic subunit. The protein encoded by this gene represents the catalytic subunit, which uses ATP to phosphorylate PtdIns, PtdIns4P and PtdIns(4,5)P2. This gene has been found to be oncogenic and has been implicated in cervical cancers. A pseudogene of this gene has been defined on chromosome 22. [provided by RefSeq, Apr 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIK3CANM_006218.4 linkuse as main transcriptc.-77+11586G>A intron_variant ENST00000263967.4
PIK3CAXM_006713658.5 linkuse as main transcriptc.-77+11970G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3CAENST00000263967.4 linkuse as main transcriptc.-77+11586G>A intron_variant 2 NM_006218.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0987
AC:
15001
AN:
152058
Hom.:
1184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.0811
Gnomad AMR
AF:
0.0755
Gnomad ASJ
AF:
0.126
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.0149
Gnomad FIN
AF:
0.0171
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.0637
Gnomad OTH
AF:
0.107
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0987
AC:
15016
AN:
152176
Hom.:
1186
Cov.:
32
AF XY:
0.0946
AC XY:
7041
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.205
Gnomad4 AMR
AF:
0.0755
Gnomad4 ASJ
AF:
0.126
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.0147
Gnomad4 FIN
AF:
0.0171
Gnomad4 NFE
AF:
0.0637
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0772
Hom.:
214
Bravo
AF:
0.111
Asia WGS
AF:
0.0220
AC:
77
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.7
DANN
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs4855094; hg19: chr3-178877977; API