rs201655779

chr19-18156170-C-Gchr19-18156170-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_005027.4(PIK3R2):c.291C>G(p.Pro97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P97P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PIK3R2 NM_005027.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.36

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 Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP7: Synonymous conserved (PhyloP=-5.36 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3R2	NM_005027.4	c.291C>G	p.Pro97=	synonymous_variant	2/16	ENST00000222254.13
PIK3R2	NR_073517.2	n.846C>G		non_coding_transcript_exon_variant	2/16
PIK3R2	NR_162071.1	n.846C>G		non_coding_transcript_exon_variant	2/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3R2	ENST00000222254.13	c.291C>G	p.Pro97=	synonymous_variant	2/16	1	NM_005027.4	P1
PIK3R2	ENST00000617130.5	c.291C>G	p.Pro97=	synonymous_variant, NMD_transcript_variant	2/15	1
PIK3R2	ENST00000426902.5	c.291C>G	p.Pro97=	synonymous_variant, NMD_transcript_variant	1/15	2
PIK3R2	ENST00000617642.2	c.291C>G	p.Pro97=	synonymous_variant, NMD_transcript_variant	2/14	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	0.11
Dann	Benign	0.75

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: rs201655779; hg19: chr19-18266980;