Genetic Variant PIK3CA:c.1747-13T>C (chr3-179219558-T-C) – ACMG Classification: Benign (-20 pts)

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

Publications

7 publications found

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 Gene-Disease associations (from GenCC):

overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
megalencephaly-capillary malformation-polymicrogyria syndrome
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
vascular malformation
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
Cowden disease
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Cowden syndrome 5
Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
hereditary breast carcinoma
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
familial ovarian cancer
Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

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 VariationId is 259959.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006218.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3CA	NM_006218.4	MANE Select	c.1747-13T>C		intron	N/A	NP_006209.2	P42336

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PIK3CA	ENST00000263967.4	TSL:2 MANE Select	c.1747-13T>C	intron	N/A	ENSP00000263967.3	P42336
PIK3CA	ENST00000955190.1		c.1777-13T>C	intron	N/A	ENSP00000625249.1
PIK3CA	ENST00000876545.1		c.1747-13T>C	intron	N/A	ENSP00000546604.1

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

African (AFR)

AF:

0.0410

AC:

1066

AN:

26012

American (AMR)

AF:

0.0394

AC:

1549

AN:

39272

Ashkenazi Jewish (ASJ)

AF:

0.0862

AC:

1968

AN:

22842

East Asian (EAS)

AF:

0.0000529

AC:

AN:

37776

South Asian (SAS)

AF:

0.0122

AC:

925

AN:

75596

European-Finnish (FIN)

AF:

0.0609

AC:

3191

AN:

52380

Middle Eastern (MID)

AF:

0.0483

AC:

241

AN:

4990

European-Non Finnish (NFE)

AF:

0.0518

AC:

41939

AN:

808950

Other (OTH)

AF:

0.0501

AC:

2426

AN:

48376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

2487

4974

7461

9948

12435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

African (AFR)

AF:

0.0417

AC:

1733

AN:

41540

American (AMR)

AF:

0.0510

AC:

779

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0869

AC:

301

AN:

3462

East Asian (EAS)

AF:

0.000386

AC:

AN:

5180

South Asian (SAS)

AF:

0.0116

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0742

AC:

786

AN:

10594

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0572

AC:

3883

AN:

67896

Other (OTH)

AF:

0.0687

AC:

145

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

368

736

1105

1473

1841

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

not provided (2)

Cowden syndrome (1)

Cowden syndrome 5 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over