rs361084

Variant names:

• chr3-138707586-T-A
• rs361084
• NM_006219.3:c.1400-297A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-138707586-T-A
• chr3-138707586-T-C
• chr3-138707586-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001256045.2(PIK3CB):​c.-311A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PIK3CB NM_001256045.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87
• Publications: 6 publications found

Genes affected

PIK3CB (HGNC:8976): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) This gene encodes an isoform of the catalytic subunit of phosphoinositide 3-kinase (PI3K). These kinases are important in signaling pathways involving receptors on the outer membrane of eukaryotic cells and are named for their catalytic subunit. The encoded protein is the catalytic subunit for PI3Kbeta (PI3KB). PI3KB has been shown to be part of the activation pathway in neutrophils which have bound immune complexes at sites of injury or infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256045.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3CB	NM_006219.3	MANE Select	c.1400-297A>T		intron	N/A	NP_006210.1	P42338
	PIK3CB	NM_001256045.2		c.-311A>T		5_prime_UTR	Exon 1 of 13	NP_001242974.1
	PIK3CB	NM_001437286.1		c.1400-297A>T		intron	N/A	NP_001424215.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3CB	ENST00000674063.1	MANE Select	c.1400-297A>T		intron	N/A	ENSP00000501150.1	P42338
	PIK3CB	ENST00000477593.6	TSL:5	c.1400-297A>T		intron	N/A	ENSP00000418143.1	P42338
	PIK3CB	ENST00000894539.1		c.1400-297A>T		intron	N/A	ENSP00000564598.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 957474 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 450562

African (AFR) AF: 0.00 AC: 0 AN: 18644

American (AMR) AF: 0.00 AC: 0 AN: 4054

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9870

East Asian (EAS) AF: 0.00 AC: 0 AN: 10008

South Asian (SAS) AF: 0.00 AC: 0 AN: 30292

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7432

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2210

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 839432

Other (OTH) AF: 0.00 AC: 0 AN: 35532

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.087
DANN	Benign	0.41
PhyloP100		-3.9

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: rs361084; hg19: chr3-138426428;