rs10515070

Positions:

• chr5-68229747-T-A

Variant summary

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

The NM_181523.3(PIK3R1):​c.334+2738T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,058 control chromosomes in the GnomAD database, including 9,199 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 0.33 (9199 hom., cov: 32)
• Consequence: PIK3R1 NM_181523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIK3R1	NM_181523.3	c.334+2738T>A		intron_variant		ENST00000521381.6	NP_852664.1
PIK3R1	XM_005248542.4	c.334+2738T>A		intron_variant			XP_005248599.1
PIK3R1	XM_017009585.3	c.334+2738T>A		intron_variant			XP_016865074.1
PIK3R1	XM_047417315.1	c.334+2738T>A		intron_variant			XP_047273271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIK3R1	ENST00000521381.6	c.334+2738T>A		intron_variant		1	NM_181523.3	ENSP00000428056	P1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50184 AN: 151940 Hom.: 9165 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.331 AC: 50269 AN: 152058 Hom.: 9199 Cov.: 32 AF XY: 0.334 AC XY: 24799 AN XY: 74330

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.313

Alfa AF: 0.292 Hom.: 890

Bravo AF: 0.342

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.43

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: rs10515070; hg19: chr5-67525575; COSMIC: COSV57126711; COSMIC: COSV57126711;