rs587686

chr18-42069586-A-Cchr18-42069586-A-Gchr18-42069586-A-T

Variant summary

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

The NM_002647.4(PIK3C3):c.2649+2073A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,028 control chromosomes in the GnomAD database, including 21,160 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 0.50 (21160 hom., cov: 32)
• Consequence: PIK3C3 NM_002647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

PIK3C3 (HGNC:8974): (phosphatidylinositol 3-kinase catalytic subunit type 3) Enables 1-phosphatidylinositol-3-kinase activity. Involved in early endosome to late endosome transport and regulation of cytokinesis. Acts upstream of or within autophagy and protein lipidation. Located in autolysosome; late endosome; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -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 = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3C3	NM_002647.4	c.2649+2073A>C		intron_variant		ENST00000262039.9
PIK3C3	NM_001308020.2	c.2460+2073A>C		intron_variant
PIK3C3	XM_047437550.1	c.2091+2073A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3C3	ENST00000262039.9	c.2649+2073A>C		intron_variant		1	NM_002647.4	P1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76461 AN: 151910 Hom.: 21107 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.504 AC: 76578 AN: 152028 Hom.: 21160 Cov.: 32 AF XY: 0.506 AC XY: 37595 AN XY: 74312

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.465

Alfa AF: 0.365 Hom.: 2215

Bravo AF: 0.526

Asia WGS AF: 0.596 AC: 2077 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	0.27
Dann	Benign	0.35

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: rs587686; hg19: chr18-39649550;