NM_003629.4:c.106+9632A>G

Variant names:

• chr1-46122215-T-C
• rs785495
• NM_003629.4:c.106+9632A>G

Variant summary

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

The NM_003629.4(PIK3R3):​c.106+9632A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,030 control chromosomes in the GnomAD database, including 15,337 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 0.45 (15337 hom., cov: 32)
• Consequence: PIK3R3 NM_003629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 13 publications found

Genes affected

PIK3R3 (HGNC:8981): (phosphoinositide-3-kinase regulatory subunit 3) Phosphatidylinositol 3-kinase (PI3K) phosphorylates phosphatidylinositol and similar compounds, which then serve as second messengers in growth signaling pathways. PI3K is composed of a catalytic and a regulatory subunit. The protein encoded by this gene represents a regulatory subunit of PI3K. The encoded protein contains two SH2 domains through which it binds activated protein tyrosine kinases to regulate their activity. [provided by RefSeq, Jun 2016]

P3R3URF-PIK3R3 (HGNC:54999): (P3R3URF-PIK3R3 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring genes LOC110117498 and PIK3R3. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Apr 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003629.4. 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
	PIK3R3	NM_003629.4	MANE Select	c.106+9632A>G		intron	N/A	NP_003620.3
	P3R3URF-PIK3R3	NM_001303427.2		c.245-41465A>G		intron	N/A	NP_001290356.1
	PIK3R3	NM_001303428.1		c.157+9632A>G		intron	N/A	NP_001290357.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3R3	ENST00000262741.10	TSL:1 MANE Select	c.106+9632A>G		intron	N/A	ENSP00000262741.5
	P3R3URF-PIK3R3	ENST00000540385.2	TSL:2	c.245-41465A>G		intron	N/A	ENSP00000439913.1
	PIK3R3	ENST00000372006.5	TSL:1	c.106+9632A>G		intron	N/A	ENSP00000361075.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67916 AN: 151912 Hom.: 15352 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.447 AC: 67895 AN: 152030 Hom.: 15337 Cov.: 32 AF XY: 0.447 AC XY: 33244 AN XY: 74306

African (AFR) AF: 0.420 AC: 17428 AN: 41446

American (AMR) AF: 0.490 AC: 7488 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3188 AN: 5182

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4405 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30130 AN: 67980

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.444 Hom.: 7808

Bravo AF: 0.451

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		1.9
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: rs785495; hg19: chr1-46587887; COSMIC: COSV53106081;