rs41273619

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006218.4(PIK3CA):c.1747-13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 1,268,272 control chromosomes in the GnomAD database, including 1,578 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.051 ( 211 hom., cov: 32)

Exomes 𝑓: 0.048 ( 1367 hom. )

Consequence

PIK3CA
NM_006218.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 1.80

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]

PIK3CA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 3-179219558-T-C is Benign according to our data. Variant chr3-179219558-T-C is described in ClinVar as [Benign]. Clinvar id is 259959.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-179219558-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIK3CA	NM_006218.4 link	c.1747-13T>C		intron_variant	Intron 11 of 20	ENST00000263967.4	NP_006209.2	P42336Q4LE51
PIK3CA	XM_006713658.5 link	c.1747-13T>C		intron_variant	Intron 11 of 20		XP_006713721.1	P42336Q4LE51

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIK3CA	ENST00000263967.4 link	c.1747-13T>C		intron_variant	Intron 11 of 20	2	NM_006218.4	ENSP00000263967.3		P42336

Frequencies

GnomAD3 genomes

AF:

0.0510

AC:

7748

AN:

151960

Hom.:

212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0418

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0511

Gnomad ASJ

AF:

0.0869

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0116

Gnomad FIN

AF:

0.0742

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0699

GnomAD2 exomes

AF:

0.0469

AC:

10621

AN:

226646

AF XY:

0.0470

show subpopulations

Gnomad AFR exome

AF:

0.0426

Gnomad AMR exome

AF:

0.0379

Gnomad ASJ exome

AF:

0.0893

Gnomad EAS exome

AF:

0.0000593

Gnomad FIN exome

AF:

0.0655

Gnomad NFE exome

AF:

0.0594

Gnomad OTH exome

AF:

0.0524

GnomAD4 exome

AF:

0.0478

AC:

53307

AN:

1116194

Hom.:

1367

Cov.:

AF XY:

0.0471

AC XY:

26727

AN XY:

567718

show subpopulations

Gnomad4 AFR exome

AF:

0.0410

AC:

1066

AN:

26012

Gnomad4 AMR exome

AF:

0.0394

AC:

1549

AN:

39272

Gnomad4 ASJ exome

AF:

0.0862

AC:

1968

AN:

22842

Gnomad4 EAS exome

AF:

0.0000529

AC:

AN:

37776

Gnomad4 SAS exome

AF:

0.0122

AC:

925

AN:

75596

Gnomad4 FIN exome

AF:

0.0609

AC:

3191

AN:

52380

Gnomad4 NFE exome

AF:

0.0518

AC:

41939

AN:

808950

Gnomad4 Remaining exome

AF:

0.0501

AC:

2426

AN:

48376

Heterozygous variant carriers

2487

4974

7461

9948

12435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

1250

2500

3750

5000

6250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0510

AC:

7749

AN:

152078

Hom.:

211

Cov.:

AF XY:

0.0508

AC XY:

3774

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0417

AC:

0.0417188

AN:

0.0417188

Gnomad4 AMR

AF:

0.0510

AC:

0.0510217

AN:

0.0510217

Gnomad4 ASJ

AF:

0.0869

AC:

0.086944

AN:

0.086944

Gnomad4 EAS

AF:

0.000386

AC:

0.0003861

AN:

0.0003861

Gnomad4 SAS

AF:

0.0116

AC:

0.0116134

AN:

0.0116134

Gnomad4 FIN

AF:

0.0742

AC:

0.0741929

AN:

0.0741929

Gnomad4 NFE

AF:

0.0572

AC:

0.0571904

AN:

0.0571904

Gnomad4 OTH

AF:

0.0687

AC:

0.0687204

AN:

0.0687204

Heterozygous variant carriers

368

736

1105

1473

1841

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0575

Hom.:

Bravo

AF:

0.0506

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 06, 2018

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Jul 26, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Cowden syndrome 5

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Cowden syndrome

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.59

Mutation Taster

=100/0

polymorphism (auto)

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over