chr10-96608076-C-T

Position:

• chr10-96608076-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.2170+1636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,134 control chromosomes in the GnomAD database, including 51,426 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 0.82 (51426 hom., cov: 31)
• Consequence: PIK3AP1 NM_152309.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3AP1	NM_152309.3	c.2170+1636G>A		intron_variant		ENST00000339364.10
PIK3AP1	XM_005269499.2	c.1636+1636G>A		intron_variant
PIK3AP1	XM_011539248.2	c.2170+1636G>A		intron_variant
PIK3AP1	XM_047424566.1	c.1636+1636G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3AP1	ENST00000339364.10	c.2170+1636G>A		intron_variant		1	NM_152309.3	P1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124710 AN: 152016 Hom.: 51375 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.820 AC: 124820 AN: 152134 Hom.: 51426 Cov.: 31 AF XY: 0.821 AC XY: 61098 AN XY: 74392

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.832

Alfa AF: 0.811 Hom.: 5511

Bravo AF: 0.824

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.57

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: rs912485; hg19: chr10-98367833;