chr5-68282917-A-G

Variant names:

• chr5-68282917-A-G
• rs34306
• NM_181523.3:c.916+1911A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181523.3(PIK3R1):​c.916+1911A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,300 control chromosomes in the GnomAD database, including 57,834 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 0.87 (57834 hom., cov: 33)
• Consequence: PIK3R1 NM_181523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 12 publications found

Genes affected

PIK3R1 (HGNC:8979): (phosphoinositide-3-kinase regulatory subunit 1) Phosphatidylinositol 3-kinase phosphorylates the inositol ring of phosphatidylinositol at the 3-prime position. The enzyme comprises a 110 kD catalytic subunit and a regulatory subunit of either 85, 55, or 50 kD. This gene encodes the 85 kD regulatory subunit. Phosphatidylinositol 3-kinase plays an important role in the metabolic actions of insulin, and a mutation in this gene has been associated with insulin resistance. Alternative splicing of this gene results in four transcript variants encoding different isoforms. [provided by RefSeq, Jun 2011]

PIK3R1 Gene-Disease associations (from GenCC):

• immunodeficiency 36 with lymphoproliferation

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
• SHORT syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet
• agammaglobulinemia 7, autosomal recessive

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• activated PI3K-delta syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181523.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3R1	NM_181523.3	MANE Select	c.916+1911A>G		intron	N/A	NP_852664.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3R1	ENST00000521381.6	TSL:1 MANE Select	c.916+1911A>G		intron	N/A	ENSP00000428056.1
	PIK3R1	ENST00000697461.1		c.916+1911A>G		intron	N/A	ENSP00000513319.1
	PIK3R1	ENST00000517643.2	TSL:3	c.916+1911A>G		intron	N/A	ENSP00000513333.1

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132117 AN: 152182 Hom.: 57789 Cov.: 33

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.868 AC: 132211 AN: 152300 Hom.: 57834 Cov.: 33 AF XY: 0.868 AC XY: 64653 AN XY: 74480

African (AFR) AF: 0.966 AC: 40159 AN: 41574

American (AMR) AF: 0.769 AC: 11773 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2853 AN: 3468

East Asian (EAS) AF: 0.760 AC: 3934 AN: 5174

South Asian (SAS) AF: 0.869 AC: 4194 AN: 4828

European-Finnish (FIN) AF: 0.885 AC: 9387 AN: 10608

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57086 AN: 68026

Other (OTH) AF: 0.851 AC: 1800 AN: 2114

Alfa AF: 0.842 Hom.: 79642

Bravo AF: 0.857

Asia WGS AF: 0.863 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34306; hg19: chr5-67578745; COSMIC: COSV57127062; COSMIC: COSV57127062;