rs7641889

chr3-179168821-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006218.4(PIK3CA):c.-77+20218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,050 control chromosomes in the GnomAD database, including 597 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 0.085 (597 hom., cov: 32)
• Consequence: PIK3CA NM_006218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3CA	NM_006218.4	c.-77+20218C>T		intron_variant		ENST00000263967.4
PIK3CA	XM_006713658.5	c.-77+20602C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3CA	ENST00000263967.4	c.-77+20218C>T		intron_variant		2	NM_006218.4	P1

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12976 AN: 151932 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0855 AC: 12995 AN: 152050 Hom.: 597 Cov.: 32 AF XY: 0.0868 AC XY: 6450 AN XY: 74336

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0763

Alfa AF: 0.0753 Hom.: 222

Bravo AF: 0.0891

Asia WGS AF: 0.0760 AC: 265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.1
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs7641889; hg19: chr3-178886609;