rs10770367

Variant names:

• chr12-18510988-C-A
• rs10770367
• NM_001288772.2:c.3323+5527C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-18510988-C-A
• chr12-18510988-C-G
• chr12-18510988-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001288772.2(PIK3C2G):​c.3323+5527C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,824 control chromosomes in the GnomAD database, including 13,744 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 0.42 (13744 hom., cov: 32)
• Consequence: PIK3C2G NM_001288772.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 8 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001288772.2. 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
	PIK3C2G	NM_001288772.2	MANE Select	c.3323+5527C>A		intron	N/A	NP_001275701.1	O75747-1
	PIK3C2G	NM_004570.6		c.3200+5527C>A		intron	N/A	NP_004561.3	O75747-2
	PIK3C2G	NM_001288774.2		c.2657+5527C>A		intron	N/A	NP_001275703.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3C2G	ENST00000538779.6	TSL:5 MANE Select	c.3323+5527C>A		intron	N/A	ENSP00000445381.1	O75747-1
	PIK3C2G	ENST00000546003.5	TSL:1	n.*2620+5527C>A		intron	N/A	ENSP00000441618.1	F5GWG6
	PIK3C2G	ENST00000675017.1		c.3323+5527C>A		intron	N/A	ENSP00000501889.1	O75747-1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63380 AN: 151708 Hom.: 13725 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.418 AC: 63449 AN: 151824 Hom.: 13744 Cov.: 32 AF XY: 0.426 AC XY: 31591 AN XY: 74216

African (AFR) AF: 0.443 AC: 18314 AN: 41386

American (AMR) AF: 0.482 AC: 7370 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3231 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1428 AN: 4794

European-Finnish (FIN) AF: 0.532 AC: 5612 AN: 10546

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25096 AN: 67884

Other (OTH) AF: 0.381 AC: 803 AN: 2106

Alfa AF: 0.383 Hom.: 28173

Bravo AF: 0.417

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10770367; hg19: chr12-18663922;