rs526219

chr10-96691349-C-T

Variant summary

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

The NM_152309.3(PIK3AP1):c.430+18218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,046 control chromosomes in the GnomAD database, including 26,331 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 0.57 (26331 hom., cov: 32)
• Consequence: PIK3AP1 NM_152309.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

PIK3AP1 (HGNC:30034): (phosphoinositide-3-kinase adaptor protein 1) Predicted to enable phosphatidylinositol 3-kinase regulatory subunit binding activity and signaling receptor binding activity. Predicted to be involved in regulation of inflammatory response; regulation of signal transduction; and toll-like receptor signaling pathway. Predicted to be located in cytoplasm and membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3AP1	NM_152309.3	c.430+18218G>A		intron_variant		ENST00000339364.10
PIK3AP1	XM_005269499.2	c.-105+9454G>A		intron_variant
PIK3AP1	XM_011539248.2	c.430+18218G>A		intron_variant
PIK3AP1	XM_047424566.1	c.-105+18218G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3AP1	ENST00000339364.10	c.430+18218G>A		intron_variant		1	NM_152309.3	P1
PIK3AP1	ENST00000468783.1	n.76+9454G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86606 AN: 151928 Hom.: 26290 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.570 AC: 86704 AN: 152046 Hom.: 26331 Cov.: 32 AF XY: 0.568 AC XY: 42197 AN XY: 74328

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.600

Alfa AF: 0.495 Hom.: 3396

Bravo AF: 0.594

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	3.2
Dann	Benign	0.48

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: rs526219; hg19: chr10-98451106; COSMIC: COSV59530858;