rs2067135

chr5-68216763-A-AAACCACAGCTCTAACACTAGTGAGCTCTchr5-68216763-A-AAACCACAGCTCTAACATTAGTGAGCTCT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_181523.3(PIK3R1):c.-387+829_-387+830insACTAGTGAGCTCTAACCACAGCTCTAAC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21821 hom., cov: 0)
• Consequence: PIK3R1 NM_181523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3R1	NM_181523.3	c.-387+829_-387+830insACTAGTGAGCTCTAACCACAGCTCTAAC		intron_variant		ENST00000521381.6
PIK3R1	XM_017009585.3	c.-654_-653insACTAGTGAGCTCTAACCACAGCTCTAAC		5_prime_UTR_variant	1/16
PIK3R1	XM_047417315.1	c.-1407_-1406insACTAGTGAGCTCTAACCACAGCTCTAAC		5_prime_UTR_variant	1/16
PIK3R1	XM_005248542.4	c.-387+825_-387+826insACTAGTGAGCTCTAACCACAGCTCTAAC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3R1	ENST00000521381.6	c.-387+829_-387+830insACTAGTGAGCTCTAACCACAGCTCTAAC		intron_variant		1	NM_181523.3	P1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78416 AN: 151050 Hom.: 21760 Cov.: 0

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.520 AC: 78540 AN: 151168 Hom.: 21821 Cov.: 0 AF XY: 0.517 AC XY: 38173 AN XY: 73866

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.459

Alfa AF: 0.406 Hom.: 1381

ClinVar

Not reported in ClinVar

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: rs2067135; hg19: chr5-67512591;