19-18155196-C-CAA

Variant summary

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

The NM_005027.4(PIK3R2):c.-423-242_-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 0.029 (143 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-CAA is Benign according to our data. Variant chr19-18155196-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1267586.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3R2	NM_005027.4	c.-423-242_-423-241dup		intron_variant		ENST00000222254.13
PIK3R2	NR_073517.2	n.133-242_133-241dup		intron_variant, non_coding_transcript_variant
PIK3R2	NR_162071.1	n.133-242_133-241dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3R2	ENST00000222254.13	c.-423-242_-423-241dup		intron_variant		1	NM_005027.4	P1
PIK3R2	ENST00000617130.5	c.-423-242_-423-241dup		intron_variant, NMD_transcript_variant		1
PIK3R2	ENST00000617642.2	c.-423-242_-423-241dup		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 3155 AN: 108690 Hom.: 143 Cov.: 0

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.00389

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0189

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.00946

Gnomad MID AF: 0.0282

Gnomad NFE AF: 0.00946

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0291 AC: 3162 AN: 108646 Hom.: 143 Cov.: 0 AF XY: 0.0298 AC XY: 1490 AN XY: 49936

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0189

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.00946

Gnomad4 NFE AF: 0.00946

Gnomad4 OTH AF: 0.0201

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

Aug 26, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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;