Variant chr12-18282464-GCCC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_001288772.2(PIK3C2G):c.385_387del(p.Pro129del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,607,454 control chromosomes in the GnomAD database, including 126,344 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 9525 hom., cov: 0)

Exomes 𝑓: 0.40 ( 116819 hom. )

Consequence

PIK3C2G
NM_001288772.2 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.60

Variant links:

Genes affected

PIK3C2G (HGNC:8973): (phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma) The protein encoded by this gene belongs to the phosphoinositide 3-kinase (PI3K) family. PI3-kinases play roles in signaling pathways involved in cell proliferation, oncogenic transformation, cell survival, cell migration, and intracellular protein trafficking. This protein contains a lipid kinase catalytic domain as well as a C-terminal C2 domain, a characteristic of class II PI3-kinases. C2 domains act as calcium-dependent phospholipid binding motifs that mediate translocation of proteins to membranes, and may also mediate protein-protein interactions. This gene may play a role in several diseases, including type II diabetes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

PIK3C2G links:

RERGL (HGNC:26213): (RERG like) Predicted to enable G protein activity and GTP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

RERGL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001288772.2. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 12-18282464-GCCC-G is Benign according to our data. Variant chr12-18282464-GCCC-G is described in ClinVar as [Benign]. Clinvar id is 1258527.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIK3C2G	NM_001288772.2 linkuse as main transcript	c.385_387del	p.Pro129del	inframe_deletion	2/33	ENST00000538779.6	NP_001275701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIK3C2G	ENST00000538779.6 linkuse as main transcript	c.385_387del	p.Pro129del	inframe_deletion	2/33	5	NM_001288772.2	ENSP00000445381	P1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52513

AN:

151674

Hom.:

9526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.503

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.299

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.364

GnomAD3 exomes

AF:

0.376

AC:

93251

AN:

248102

Hom.:

18099

AF XY:

0.376

AC XY:

50626

AN XY:

134608

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.387

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.268

Gnomad SAS exome

AF:

0.339

Gnomad FIN exome

AF:

0.440

Gnomad NFE exome

AF:

0.410

Gnomad OTH exome

AF:

0.384

GnomAD4 exome

AF:

0.396

AC:

576981

AN:

1455660

Hom.:

116819

AF XY:

0.395

AC XY:

286059

AN XY:

724392

show subpopulations

Gnomad4 AFR exome

AF:

0.214

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.372

Gnomad4 EAS exome

AF:

0.257

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.434

Gnomad4 NFE exome

AF:

0.412

Gnomad4 OTH exome

AF:

0.377

GnomAD4 genome

AF:

0.346

AC:

52513

AN:

151794

Hom.:

9525

Cov.:

AF XY:

0.345

AC XY:

25609

AN XY:

74156

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.369

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.276

Gnomad4 SAS

AF:

0.329

Gnomad4 FIN

AF:

0.434

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.381

Hom.:

2072

Bravo

AF:

0.339

Asia WGS

AF:

0.282

AC:

981

AN:

3478

EpiCase

AF:

0.403

EpiControl

AF:

0.409

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 16, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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