10-96608076-C-T

Variant names:

• chr10-96608076-C-T
• rs912485
• NM_152309.3:c.2170+1636G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152309.3. 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
	PIK3AP1	NM_152309.3	MANE Select	c.2170+1636G>A		intron	N/A	NP_689522.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3AP1	ENST00000339364.10	TSL:1 MANE Select	c.2170+1636G>A		intron	N/A	ENSP00000339826.5	Q6ZUJ8-1
	PIK3AP1	ENST00000371109.3	TSL:1	c.967+1636G>A		intron	N/A	ENSP00000360150.3	Q6ZUJ8-3
	PIK3AP1	ENST00000866991.1		c.2170+1636G>A		intron	N/A	ENSP00000537050.1

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

African (AFR) AF: 0.750 AC: 31105 AN: 41468

American (AMR) AF: 0.885 AC: 13531 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2966 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5133 AN: 5182

South Asian (SAS) AF: 0.873 AC: 4211 AN: 4824

European-Finnish (FIN) AF: 0.816 AC: 8651 AN: 10596

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56553 AN: 67994

Other (OTH) AF: 0.832 AC: 1754 AN: 2108

Alfa AF: 0.808 Hom.: 5731

Bravo AF: 0.824

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.57
PhyloP100		-0.82
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: rs912485; hg19: chr10-98367833;