rs251406

chr5-68240633-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181523.3(PIK3R1):c.334+13624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,140 control chromosomes in the GnomAD database, including 42,070 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 0.74 (42070 hom., cov: 32)
• Consequence: PIK3R1 NM_181523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3R1	NM_181523.3	c.334+13624A>G		intron_variant		ENST00000521381.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3R1	ENST00000521381.6	c.334+13624A>G		intron_variant		1	NM_181523.3	P1

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112777 AN: 152022 Hom.: 42030 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.742 AC: 112866 AN: 152140 Hom.: 42070 Cov.: 32 AF XY: 0.743 AC XY: 55261 AN XY: 74370

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.732

Alfa AF: 0.710 Hom.: 34203

Bravo AF: 0.752

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	0.047
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs251406; hg19: chr5-67536461;