19-18155196-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005027.4(PIK3R2):c.-423-241dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.82 (36458 hom., cov: 0)
• Consequence: PIK3R2 NM_005027.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.181

Genes affected

PIK3R2 (HGNC:8980): (phosphoinositide-3-kinase regulatory subunit 2) Phosphatidylinositol 3-kinase (PI3K) is a lipid kinase that phosphorylates phosphatidylinositol and similar compounds, creating second messengers important in growth signaling pathways. PI3K functions as a heterodimer of a regulatory and a catalytic subunit. The protein encoded by this gene is a regulatory component of PI3K. Three transcript variants, one protein coding and the other two non-protein coding, have been found for this gene. [provided by RefSeq, Apr 2019]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-18155196-C-CA is Benign according to our data. Variant chr19-18155196-C-CA is described in ClinVar as [Benign]. Clinvar id is 1229650.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3R2	NM_005027.4	c.-423-241dup		intron_variant		ENST00000222254.13
PIK3R2	NR_073517.2	n.133-241dup		intron_variant, non_coding_transcript_variant
PIK3R2	NR_162071.1	n.133-241dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3R2	ENST00000222254.13	c.-423-241dup		intron_variant		1	NM_005027.4	P1
PIK3R2	ENST00000617130.5	c.-423-241dup		intron_variant, NMD_transcript_variant		1
PIK3R2	ENST00000617642.2	c.-423-241dup		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.817 AC: 89211 AN: 109212 Hom.: 36478 Cov.: 0

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.817 AC: 89169 AN: 109168 Hom.: 36458 Cov.: 0 AF XY: 0.816 AC XY: 40943 AN XY: 50196

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.834

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs34249019; hg19: chr19-18266006;