Genetic Variant PIK3CA-DT:n.58+2838T>C (chr3-179145078-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000435560.1(PIK3CA-DT):n.58+2838T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,134 control chromosomes in the GnomAD database, including 5,802 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 0.25 ( 5802 hom., cov: 32)

Consequence

PIK3CA-DT
ENST00000435560.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.726

Publications

6 publications found

Variant links:

Genes affected

PIK3CA-DT (HGNC:52932): (PIK3CA divergent transcript)

PIK3CA-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIK3CA-DT	NR_125401.1 link	n.58+2838T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PIK3CA-DT	ENST00000435560.1 link	n.58+2838T>C	intron_variant	Intron 1 of 2	1
PIK3CA-DT	ENST00000822433.1 link	n.104+2838T>C	intron_variant	Intron 1 of 3
PIK3CA-DT	ENST00000822434.1 link	n.85+2838T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38201

AN:

152016

Hom.:

5792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.251

AC:

38254

AN:

152134

Hom.:

5802

Cov.:

AF XY:

0.249

AC XY:

18533

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.421

AC:

17473

AN:

41474

American (AMR)

AF:

0.226

AC:

3458

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

872

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

521

AN:

5182

South Asian (SAS)

AF:

0.238

AC:

1147

AN:

4826

European-Finnish (FIN)

AF:

0.159

AC:

1684

AN:

10580

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.180

AC:

12207

AN:

67990

Other (OTH)

AF:

0.250

AC:

529

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1340

2680

4021

5361

6701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<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:

0.234

Hom.:

1746

Bravo

AF:

0.267

Asia WGS

AF:

0.181

AC:

630

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.76

(source)

DANN

Benign

0.62

PhyloP100

-0.73

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over