rs7895244

chr10-96672946-T-A

Variant summary

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

The NM_152309.3(PIK3AP1):c.431-16012A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,226 control chromosomes in the GnomAD database, including 1,805 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 0.12 (1805 hom., cov: 32)
• Consequence: PIK3AP1 NM_152309.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3AP1	NM_152309.3	c.431-16012A>T		intron_variant		ENST00000339364.10
PIK3AP1	XM_005269499.2	c.-104-16012A>T		intron_variant
PIK3AP1	XM_011539248.2	c.431-16012A>T		intron_variant
PIK3AP1	XM_047424566.1	c.-104-16012A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3AP1	ENST00000339364.10	c.431-16012A>T		intron_variant		1	NM_152309.3	P1
PIK3AP1	ENST00000468783.1	n.77-16012A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18118 AN: 152108 Hom.: 1798 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.119 AC: 18151 AN: 152226 Hom.: 1805 Cov.: 32 AF XY: 0.118 AC XY: 8790 AN XY: 74442

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0819 Hom.: 130

Bravo AF: 0.140

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.5
Dann	Benign	0.75

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: rs7895244; hg19: chr10-98432703;