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12-18282464-GCCC-G

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

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Nonframeshift variant in NON repetitive region in NM_001288772.2. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
PIK3C2GNM_001288772.2 linkuse as main transcriptc.385_387del p.Pro129del inframe_deletion 2/33 ENST00000538779.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3C2GENST00000538779.6 linkuse as main transcriptc.385_387del p.Pro129del inframe_deletion 2/335 NM_001288772.2 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.346
AC:
52513
AN:
151674
Hom.:
9526
Cov.:
0
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.346
AC:
52513
AN:
151794
Hom.:
9525
Cov.:
0
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 submitterclinical testingGeneDxAug 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.

Other links and lift over

dbSNP: rs35277916; hg19: chr12-18435398; API