rs10841025

Positions:

• chr12-18426910-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001288772.2(PIK3C2G):​c.2504+2871C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,084 control chromosomes in the GnomAD database, including 3,956 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 0.22 (3956 hom., cov: 32)
• Consequence: PIK3C2G NM_001288772.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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]

LOC124902891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3C2G	NM_001288772.2	c.2504+2871C>A		intron_variant		ENST00000538779.6
LOC124902891	XR_007063234.1	n.106+7040G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3C2G	ENST00000538779.6	c.2504+2871C>A		intron_variant		5	NM_001288772.2	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33668 AN: 151966 Hom.: 3947 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.222 AC: 33720 AN: 152084 Hom.: 3956 Cov.: 32 AF XY: 0.228 AC XY: 16982 AN XY: 74330

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.221

Alfa AF: 0.196 Hom.: 1545

Bravo AF: 0.226

Asia WGS AF: 0.245 AC: 851 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs10841025; hg19: chr12-18579844;