Variant chr18-42034146-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002647.4(PIK3C3):c.1839+189G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,026 control chromosomes in the GnomAD database, including 21,405 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 ( 21405 hom., cov: 32)

Consequence

PIK3C3
NM_002647.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Variant links:

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]

PIK3C3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PIK3C3	NM_002647.4 link	c.1839+189G>A	intron_variant	ENST00000262039.9	NP_002638.2	Q8NEB9
PIK3C3	NM_001308020.2 link	c.1650+189G>A	intron_variant		NP_001294949.1	A8MYT4B4DPV9
PIK3C3	XM_047437549.1 link	c.1839+189G>A	intron_variant		XP_047293505.1
PIK3C3	XM_047437550.1 link	c.1281+189G>A	intron_variant		XP_047293506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIK3C3	ENST00000262039.9 link	c.1839+189G>A		intron_variant		1	NM_002647.4	ENSP00000262039.3		Q8NEB9

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76607

AN:

151908

Hom.:

21354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.379

Gnomad MID

AF:

0.401

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.462

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

GnomAD4 genome

AF:

0.505

AC:

76720

AN:

152026

Hom.:

21405

Cov.:

AF XY:

0.507

AC XY:

37649

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.751

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.341

Gnomad4 EAS

AF:

0.611

Gnomad4 SAS

AF:

0.511

Gnomad4 FIN

AF:

0.379

Gnomad4 NFE

AF:

0.370

Gnomad4 OTH

AF:

0.466

Alfa

AF:

0.465

Hom.:

3448

Bravo

AF:

0.526

Asia WGS

AF:

0.591

AC:

2057

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.17

DANN

Benign

0.55

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over